GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Caulobacter crescentus NA1000

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate CCNA_00846 CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= reanno::SB2B:6938573
         (1058 letters)



>FitnessBrowser__Caulo:CCNA_00846
          Length = 1029

 Score =  956 bits (2470), Expect = 0.0
 Identities = 529/1027 (51%), Positives = 673/1027 (65%), Gaps = 14/1027 (1%)

Query: 31   DEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVGIDAFLQQYSLETQEG 90
            DE A + +L+A  P S E+ A + + A  LV   R+  +K  +V  ++FLQ++SL T+EG
Sbjct: 14   DEAAVIADLLAAKPLSSEDRAAVRAEAEALVRGARRSVRKQGVV--ESFLQEFSLGTREG 71

Query: 91   IILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTGKIVQL 150
            + LMCLAEALLR PD +T D LIA+K+  A W  H+  SDS+ VNASTWGLMLTGKIV+ 
Sbjct: 72   LALMCLAEALLRTPDDDTRDKLIAEKIGSADWASHLGGSDSLFVNASTWGLMLTGKIVEP 131

Query: 151  DKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAEKRKLGY 210
            D+         + +L  RLGEPVIR A+  A++IMG+QFVLGRTIE  +K AA +   G 
Sbjct: 132  DETARNDMPGFIKKLAGRLGEPVIRAAVGQAIRIMGEQFVLGRTIEAAIKRAAAE---GD 188

Query: 211  THSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALHPRYEVA 270
              S+DMLGE A T  DA +Y + YA+AI+ +G             +S+KLSAL PRYE  
Sbjct: 189  MCSFDMLGEGARTAADAARYEKAYADAIETVGKLSNGAGPEAGHGVSVKLSALCPRYEAT 248

Query: 271  NEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAKGWGLLG 330
            +EDRV  ELY   ++L + A   N+   IDAEE DRL LSLKL  KL +      W  LG
Sbjct: 249  HEDRVWEELYPRTLRLAKIAARHNLNFTIDAEEADRLALSLKLLDKLCREPELGDWTGLG 308

Query: 331  IVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYPLFTRKA 390
            + VQAY KR   V+  L  L++E G  + +RLVKGAYWDSE+K AQ AG   YP+FT K 
Sbjct: 309  LAVQAYQKRCGEVIARLKALSEETGRRLMVRLVKGAYWDSEIKRAQVAGRPDYPVFTTKP 368

Query: 391  ATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDR--KFEFQRLHGMGQEL 448
            ATD+SYL  A+ L+  A    +Y QFA+HNA T+AA+  M  +   K E QRLHGMG+ L
Sbjct: 369  ATDLSYLVNAKALIEAAPH--LYAQFATHNAHTLAAVVRMAKNTGVKIEHQRLHGMGEAL 426

Query: 449  YDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVTHP 508
            Y          T+R YAP+G H+DLLPYLVRRLLENGANTSFVH L+D + P+E +VT P
Sbjct: 427  YKAADDLYDGITLRAYAPVGGHEDLLPYLVRRLLENGANTSFVHALLDERVPVEKVVTDP 486

Query: 509  LKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPL 568
            + T++ +    + KI  P +++G  R NS GL++++ ++ E   AA+        SAGPL
Sbjct: 487  IDTVEAHPD-RHAKIPTPINVYGERRVNSAGLDLSVKADRERLSAAVAAQDGVTLSAGPL 545

Query: 569  VNGETLSGEVR-DVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRANA 627
            V G+ ++G     +++P N    VG V+ A  A I++A   A  A  +W R     RA  
Sbjct: 546  VGGKVVAGGAPLPLIAPANDQKTVGVVSEAQSAQIDEAFKLARAAQPAWDRAGGVARAQV 605

Query: 628  LQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPG 687
            L+ + D LE N E LIAL +REAGK++ DGI EVREAVDFCRYYA+ A+    + E+L G
Sbjct: 606  LRAMGDALEANIERLIALLSREAGKTLSDGIAEVREAVDFCRYYAMLAEDQFGEAEILKG 665

Query: 688  PTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQ 747
            P GE N L L GRGVFVCISPWNFPLAIF GQ+AAALA GN V+AKPAEQT LI F AV+
Sbjct: 666  PVGETNSLRLAGRGVFVCISPWNFPLAIFTGQIAAALAAGNAVLAKPAEQTPLIAFEAVK 725

Query: 748  LAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIP 807
            L H AG+   +L  LPG G  VGA LTS E + GV FTG T TA  IN+ LA R G I+P
Sbjct: 726  LYHAAGLDPRLLALLPGRGETVGAALTSHEDLDGVAFTGGTDTAWRINQTLAARQGPIVP 785

Query: 808  LIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKG 867
             IAETGG N M VD+T+Q EQV++DV+ SAF SAGQRCSALR+L+L  D A+ +++ LKG
Sbjct: 786  FIAETGGLNGMFVDTTAQREQVIDDVIVSAFGSAGQRCSALRLLFLPHDTADHIIEGLKG 845

Query: 868  AMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAP 927
            AMD L LG+P    TDVGPVIDA AK  L+ H+  +K   +++H L+ P G   G F AP
Sbjct: 846  AMDALVLGDPALAVTDVGPVIDAEAKDALDKHLVRLKSDAKVLHALAAPAG---GTFFAP 902

Query: 928  TAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALEVA 987
               EI +   L +E FGP+LHVVRYK   L+KV   + +  +GLTLGIHSR E  A +V 
Sbjct: 903  VLAEIPTADFLEREVFGPVLHVVRYKPENLEKVAGALAARRYGLTLGIHSRIESFAADVQ 962

Query: 988  DKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGG 1047
              V  GN Y+NR+  GAVVGVQPFGG+GLSGTGPKAGGPH L RF  E+  + NITA GG
Sbjct: 963  RLVPAGNAYVNRSMTGAVVGVQPFGGEGLSGTGPKAGGPHALLRFAVERALSVNITAQGG 1022

Query: 1048 NATLLSL 1054
            +  LL+L
Sbjct: 1023 DPALLNL 1029


Lambda     K      H
   0.317    0.134    0.380 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2548
Number of extensions: 99
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1058
Length of database: 1029
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 984
Effective search space:   996792
Effective search space used:   996792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

Align candidate CCNA_00846 CCNA_00846 (proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.25815.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25815.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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