Query= AAB09563.1 | calcium-activated potassium channel rSK2 [Rat-norveg (580 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences) 1,191,572 sequences; 5,115,164,321 total letters

Sequences producing significant alignments: (bits) Value gi|17933579|ref|NM_080339.1| Drosophila melanogaster small ... 272 6e-72 gi|10728478|gb|AE003434.2|AE003434 Drosophila melanogaster ... 179 7e-44 gi|18266478|gb|AC104604.5| Drosophila melanogaster X BAC RP... 179 7e-44 gi|17946110|gb|AY071475.1| Not significant from here down ... 47 4e-04

>gi|17933579|ref|NM_080339.1|   Drosophila melanogaster small conductance calcium-activated
           potassium channel (SK), mRNA!!  They Have IT WRONG!!!
          Length = 1016                 Mostly it is the K+ pore!         

 Score =  272 bits (695), Expect = 6e-72
 Identities = 128/202 (63%), Positives = 170/202 (83%)
 Frame = +2
Match starts at 336 i.e. last 2/5ths of rsk2 pep- too incomplete

 they have predicted a gene that lacks proper length and all the TM1-5

                         K+ Pore                         TM6
Query: 336 YHDQQDVTSNFLGAMWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAVVA 395
           +HD++   +N L AMWLI+ITFLS+G+GD+VPNTYCG+G+ + TGIMGAGCTAL+VAVV+
Sbjct: 2   FHDEEH--ANLLNAMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIMGAGCTALLVAVVS 175

Query: 396 RKLELTKAEKHVHNFMMDTQLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRK 455
           RKLELT+AEKHVHNFMMDTQLTKR+KNAAANVLRETWLIYK+T+LVK+++  +VR HQRK
Sbjct: 176 RKLELTRAEKHVHNFMMDTQLTKRLKNAAANVLRETWLIYKHTRLVKRVNPGRVRTHQRK 355
                Calmodulin Bndx Domain
Query: 456 FLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQNIMYDMISDLNERSEDFEKRIVTLETKL 515
           FL AI+ LR VKM+QRKL D ANT+ D+AKTQN +Y++ISD++ R +  E+R+  LE K+
Sbjct: 356 FLLAIYALRKVKMDQRKLMDNANTITDMAKTQNTVYEIISDMSSRQDAIEERLTNLEDKM 535

Query: 516 ETLIGSIHALPGLISQTIRQQQ 537
           +++   + +LP L+S+ + Q Q
Sbjct: 536 QSIQEHMESLPDLLSRCLTQHQ 601
================================================

This is the record that has it all-very important to get it right

>gi|10728478|gb|AE003434.2|AE003434   Drosophila melanogaster genomic scaffold 142000013386054 section 18 of
             35, complete sequence                       This data ^ follows from (next) BAC clone   
          Length = 302786

 Score =  179 bits (453), Expect = 7e-44
 Identities = 102/195 (52%), Positives = 116/195 (59%), Gaps = 55/195 (28%)
 Frame = +1  This means I can use 3-frame (forward translation!!

                                 TM-3

Query: 196   LFMVDNGADDWRIAMTYERIFFICLEILVCAIHPIPGNYTFTWTARLAFSYAP-STTTAD 254
             LFM+DN ADDWRIAMT++RI  I LE+ +CAIHPIPG Y F WT +LA       T    
Sbjct: 59689 LFMIDNCADDWRIAMTWQRISQIGLELFICAIHPIPGEYYFQWTTKLANKNKTIGTEMVP 59868
                  TM-4
Query: 255   VDIILSIPMFLRLYLIARVMLLHSKLFTDASSRSIGALNKIN-------FNT-------- 299
              D+ LS+PMFLRLYLI RVMLLHSKLFTDASSRSIGALN+IN       FN+        
Sbjct: 59869 YDVALSLPMFLRLYLICRVMLLHSKLFTDASSRSIGALNRINFNTR*VQFNSKM*NIRFF 60048
                                                           TM-4
Query: 300   ---------------------------------------RFVMKTLMTICPGTVLLVFSI 320
                                                    RFV+KTLMTICPGTVLLVF +
Sbjct: 60049 *NGHGHTVFQI*LRSPCAHLAIM*CNVM*FKSPHLLLHYRFVLKTLMTICPGTVLLVFMV 60228

Query: 321   SLWIIAAWTVRACER 335
             SLWIIA+WT+R CER
Sbjct: 60229 SLWIIASWTLRQCER 60273

 Score = 77.4 bits (189), Expect = 3e-13
 Identities = 36/50 (72%), Positives = 42/50 (84%)
 Frame = +2
                       TM-6                             CalModBDX   
Query: 371   CGKGVCLLTGIMGAGCTALVVAVVARKLELTKAEKHVHNFMMDTQLTKRV 420
             C      ++ + GAGCTAL+VAVV+RKLELT+AEKHVHNFMMDTQLTKRV
Sbjct: 72428 CPNSPLYMSSLQGAGCTALLVAVVSRKLELTRAEKHVHNFMMDTQLTKRV 72577

 Score = 77.0 bits (188), Expect = 4e-13
 Identities = 52/160 (32%), Positives = 72/160 (44%), Gaps = 37/160 (23%)
 Frame = +2
     NB lowest query #               TM-1
Query: 117   NIGYKLGHRRALFEKRKRLSDYALIFGMFGIVVMVIETEL-SWGAYDK------------ 163
             N+GY+LG R+ALFEKRKR+SDYAL+ GMFGI+VMVIE EL S G Y K            
Sbjct: 55004 NVGYRLGKRKALFEKRKRISDYALVMGMFGIIVMVIENELSSAGVYTKVRVLHLNVIYYS 55183
 'Hunk should start @ 45000!!                   TM-2
Query: 164   ------------------------ASLYSLALKCXXXXXXXXXXXXXXVYHAREIQLFMV 199
                                     AS YS ALK                YHA E+Q+ + 
Sbjct: 55184 TLNKR*ATQD*FVKCISIF*LHF*ASFYSTALKTLISVSTVILLGLIVAYHALEVQVRVS 55363
                                    TM-3
Query: 200   DNGADDWRIAMTYERIFFICLEILVCAIHPIPGNYTFTWT 239
              N        + ++ +    L +++     +P +++ T T
Sbjct: 55364 AN------CILLFQMLLMFLLMVVIVNCLTLPSSFSLTVT 55465

 Score = 71.6 bits (174), Expect = 2e-11
 Identities = 35/69 (50%), Positives = 50/69 (71%)
 Frame = +3
                           CalModulin binding Domain
Query: 420   VKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANT 479
             +KNAAANVLRETWLIYK+T+LVK+++  +VR HQRKFL AI+    +++ Q+ +N   N 
Sbjct: 72753 LKNAAANVLRETWLIYKHTRLVKRVNPGRVRTHQRKFLLAIYA*VFLEIYQQTINQTTNQ 72932

Query: 480   LVDLAKTQN 488
               +   T+N
Sbjct: 72933 PTNQPTTKN 72959

 Score = 71.6 bits (174), Expect = 2e-11
 Identities = 30/48 (62%), Positives = 41/48 (84%)
 Frame = +2
                           K+ Pore                     TM-6
Query: 335   RYHDQQDVTSNFLGAMWLISITFLSIGYGDMVPNTYCGKGVCLLTGIM 382
             R+HD++   +N L AMWLI+ITFLS+G+GD+VPNTYCG+G+ + TGIM
Sbjct: 70331 RFHDEEH--ANLLNAMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIM 70468

N.B.B. duplicate Query sequence above and below reveals alternative exons!!! 

 Score = 65.9 bits (159), Expect = 9e-10
 Identities = 39/110 (35%), Positives = 60/110 (54%), Gaps = 1/110 (0%)
 Frame = +3
                               K+ Pore                     TM-6  
Query: 334   ERYHDQQDVTSNFLGAMWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAV 393
             +R+HD++   +N L +MWL +ITFL +GYGD+VPNTYCG+G+ L  G         +V  
Sbjct: 64863 KRFHDEEH--ANLLNSMWLTAITFLCVGYGDIVPNTYCGRGITLTCG---------MVVS 65009
                                         Ca-Mod Bndx
Query: 394   VARKLELTKAEKHVHNFMMDTQLTKRVKNAAANVLRETWLIY-KNTKLVK 442
             ++ K +  K +K   N      L++  K   +  L   +  Y K TK +K
Sbjct: 65010 ISSKPQKKKTKKKKFNKNKTKNLSRNTKTKDSQKLHL*YR*YIKKTK*MK 65159

 Score = 36.6 bits (83), Expect = 0.59
 Identities = 16/24 (66%), Positives = 20/24 (82%)
 Frame = +3
                   Cal-Mod bndx
Query: 462   QLRSVKMEQRKLNDQANTLVDLAK 485
             +LR VKM+QRKL D ANT+ D+AK
Sbjct: 74343 RLRKVKMDQRKLMDNANTITDMAK 74414

 Score = 36.6 bits (83), Expect = 0.59
 Identities = 13/35 (37%), Positives = 27/35 (77%)
 Frame = +2
                                        Query Length=580
Query: 484   AKTQNIMYDMISDLNERSEDFEKRIVTLETKLETL 518 Biggest query #
             ++TQN +Y++ISD++ R +  E+R+  LE K++++
Sbjct: 74678 SQTQNTVYEIISDMSSRQDAIEERLTNLEDKMQSI 74782
                                     So, end of hunk ~ 80000

Thus 'hunk' for translation= ~45000 to 80000!!! And 

covers ~4/5 of rsk2 and all TM domains and 

as of this marking fits together very nicely!! I think I got it

++++++++++++++++++++++++++++++++++++++++++++++++++++++

Record below is from early BAC clone with inverse compl orientation 

and contains exactly the same sequence (how do I know that?) as marked above!!

>gi|18266478|gb|AC104604.5|  Drosophila melanogaster X BAC RP98-18K5 (Roswell Park Cancer Institute
              Drosophila BAC Library) complete sequence
          Length = 167901

 Score =  179 bits (453), Expect = 7e-44
 Identities = 102/195 (52%), Positives = 116/195 (59%), Gaps = 55/195 (28%)
 Frame = -1

Query: 196    LFMVDNGADDWRIAMTYERIFFICLEILVCAIHPIPGNYTFTWTARLAFSYAP-STTTAD 254
              LFM+DN ADDWRIAMT++RI  I LE+ +CAIHPIPG Y F WT +LA       T    
Sbjct: 113124 LFMIDNCADDWRIAMTWQRISQIGLELFICAIHPIPGEYYFQWTTKLANKNKTIGTEMVP 112945

Query: 255    VDIILSIPMFLRLYLIARVMLLHSKLFTDASSRSIGALNKIN-------FNT-------- 299
               D+ LS+PMFLRLYLI RVMLLHSKLFTDASSRSIGALN+IN       FN+        
Sbjct: 112944 YDVALSLPMFLRLYLICRVMLLHSKLFTDASSRSIGALNRINFNTR*VQFNSKM*NIRFF 112765

Query: 300    ---------------------------------------RFVMKTLMTICPGTVLLVFSI 320
                                                     RFV+KTLMTICPGTVLLVF +
Sbjct: 112764 *NGHGHTVFQI*LRSPCAHLAIM*CNVM*FKSPHLLLHYRFVLKTLMTICPGTVLLVFMV 112585

Query: 321    SLWIIAAWTVRACER 335
              SLWIIA+WT+R CER
Sbjct: 112584 SLWIIASWTLRQCER 112540

 Score = 77.4 bits (189), Expect = 3e-13
 Identities = 36/50 (72%), Positives = 42/50 (84%)
 Frame = -3

Query: 371    CGKGVCLLTGIMGAGCTALVVAVVARKLELTKAEKHVHNFMMDTQLTKRV 420
              C      ++ + GAGCTAL+VAVV+RKLELT+AEKHVHNFMMDTQLTKRV
Sbjct: 100039 CPNSPLYMSSLQGAGCTALLVAVVSRKLELTRAEKHVHNFMMDTQLTKRV 99890

 Score = 77.0 bits (188), Expect = 4e-13
 Identities = 52/160 (32%), Positives = 72/160 (44%), Gaps = 37/160 (23%)
 Frame = -2

Query: 117    NIGYKLGHRRALFEKRKRLSDYALIFGMFGIVVMVIETEL-SWGAYDK------------ 163
              N+GY+LG R+ALFEKRKR+SDYAL+ GMFGI+VMVIE EL S G Y K            
Sbjct: 117809 NVGYRLGKRKALFEKRKRISDYALVMGMFGIIVMVIENELSSAGVYTKVRVLHLNVIYYS 117630

Query: 164    ------------------------ASLYSLALKCXXXXXXXXXXXXXXVYHAREIQLFMV 199
                                      AS YS ALK                YHA E+Q+ + 
Sbjct: 117629 TLNKR*ATQD*FVKCISIF*LHF*ASFYSTALKTLISVSTVILLGLIVAYHALEVQVRVS 117450

Query: 200    DNGADDWRIAMTYERIFFICLEILVCAIHPIPGNYTFTWT 239
               N        + ++ +    L +++     +P +++ T T
Sbjct: 117449 AN------CILLFQMLLMFLLMVVIVNCLTLPSSFSLTVT 117348

 Score = 71.6 bits (174), Expect = 2e-11
 Identities = 35/69 (50%), Positives = 50/69 (71%)
 Frame = -1

Query: 420   VKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANT 479
             +KNAAANVLRETWLIYK+T+LVK+++  +VR HQRKFL AI+    +++ Q+ +N   N 
Sbjct: 99714 LKNAAANVLRETWLIYKHTRLVKRVNPGRVRTHQRKFLLAIYA*VFLEIYQQTINQTTNQ 99535

Query: 480   LVDLAKTQN 488
               +   T+N
Sbjct: 99534 PTNQPTTKN 99508

 Score = 71.6 bits (174), Expect = 2e-11
 Identities = 30/48 (62%), Positives = 41/48 (84%)
 Frame = -3

Query: 335    RYHDQQDVTSNFLGAMWLISITFLSIGYGDMVPNTYCGKGVCLLTGIM 382
              R+HD++   +N L AMWLI+ITFLS+G+GD+VPNTYCG+G+ + TGIM
Sbjct: 102136 RFHDEEH--ANLLNAMWLIAITFLSVGFGDIVPNTYCGRGIAVSTGIM 101999

 Score = 65.9 bits (159), Expect = 9e-10
 Identities = 39/110 (35%), Positives = 60/110 (54%), Gaps = 1/110 (0%)
 Frame = -3

Query: 334    ERYHDQQDVTSNFLGAMWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAV 393
              +R+HD++   +N L +MWL +ITFL +GYGD+VPNTYCG+G+ L  G         +V  
Sbjct: 107950 KRFHDEEH--ANLLNSMWLTAITFLCVGYGDIVPNTYCGRGITLTCG---------MVVS 107804

Query: 394    VARKLELTKAEKHVHNFMMDTQLTKRVKNAAANVLRETWLIY-KNTKLVK 442
              ++ K +  K +K   N      L++  K   +  L   +  Y K TK +K
Sbjct: 107803 ISSKPQKKKTKKKKFNKNKTKNLSRNTKTKDSQKLHL*YR*YIKKTK*MK 107654

 Score = 36.6 bits (83), Expect = 0.59
 Identities = 16/24 (66%), Positives = 20/24 (82%)
 Frame = -1

Query: 462   QLRSVKMEQRKLNDQANTLVDLAK 485
             +LR VKM+QRKL D ANT+ D+AK
Sbjct: 98124 RLRKVKMDQRKLMDNANTITDMAK 98053

 Score = 36.6 bits (83), Expect = 0.59
 Identities = 13/35 (37%), Positives = 27/35 (77%)
 Frame = -3

Query: 484   AKTQNIMYDMISDLNERSEDFEKRIVTLETKLETL 518
             ++TQN +Y++ISD++ R +  E+R+  LE K++++
Sbjct: 97789 SQTQNTVYEIISDMSSRQDAIEERLTNLEDKMQSI 97685