GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Shewanella loihica PV-4

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate 5210634 Shew_3062 glycine dehydrogenase (RefSeq)

Query= CharProtDB::CH_003480
         (957 letters)



>FitnessBrowser__PV4:5210634
          Length = 962

 Score = 1325 bits (3430), Expect = 0.0
 Identities = 643/961 (66%), Positives = 787/961 (81%), Gaps = 6/961 (0%)

Query: 2   TQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAP 61
           T+TL+QLE    FI RHIGPD+A QQEMLN VGA+SL  LT QIVP+ I+L     VG+ 
Sbjct: 3   TETLTQLEQHELFIRRHIGPDSADQQEMLNFVGAESLEDLTQQIVPESIRLGRDLAVGSA 62

Query: 62  ATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQ 121
             E   LA ++  A +NK F SYIGMGY    +P VI RN+ ENPGWYTAYTPYQPE++Q
Sbjct: 63  CGEAEGLASIRKYADKNKVFKSYIGMGYYGTIVPSVIQRNVFENPGWYTAYTPYQPEIAQ 122

Query: 122 GRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHP 181
           GRLEA+LNFQQ+++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FF+A DV P
Sbjct: 123 GRLEAILNFQQLSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFIADDVFP 182

Query: 182 QTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKI 241
           QT+DVV+TRAE FGFE++V  A + ++++ +FG L Q     G+I D+T L + L+ +K 
Sbjct: 183 QTIDVVKTRAECFGFEIVVGPASEAVNYE-LFGALFQYTNHYGQITDFTELFAALQEKKA 241

Query: 242 VVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRI 301
           VV+VAADIM+LV L +PG  GAD+VFGSAQRFGVPMG+GGPHAAFF  +D++KRS+PGRI
Sbjct: 242 VVTVAADIMSLVSLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVTRDQHKRSLPGRI 301

Query: 302 IGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIA 361
           IGVS+D  GN ALRMAMQTREQHIRREKANSNICT+QVLLAN+AS YAV+HGP GLK IA
Sbjct: 302 IGVSQDTRGNRALRMAMQTREQHIRREKANSNICTAQVLLANMASFYAVFHGPQGLKIIA 361

Query: 362 NRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAVG 421
           +RIHRL DI AAGL+ KG++L +  +FDT+  +VAD A    RA A E+NLR D    +G
Sbjct: 362 DRIHRLADIFAAGLKAKGVELVNNTWFDTVSFKVADSAAAQARAIAGEVNLRIDSDGILG 421

Query: 422 ITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDV-AHDSRSIQPAMLRDDEILTHPVFN 480
           + + ETTTRE+V QLF+++LG+ HGLD+  +D D+ A+ S SI   ++R D IL HP FN
Sbjct: 422 VAMAETTTREDVAQLFDIVLGEGHGLDVAAIDADIIANGSNSIPAELVRQDAILEHPTFN 481

Query: 481 RYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPE 540
           RYHSETEMMRY+  LE KDLALN +MI LGSCTMKLNAA EM+P++WPEF  +HPFCP +
Sbjct: 482 RYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAATEMMPVSWPEFGNMHPFCPQD 541

Query: 541 QAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600
           QA+GY ++I +L++WLV +TGYDA+CMQPNSGA GEYAGLLAI+ YHESR EGHR++CLI
Sbjct: 542 QAQGYAELIEELSNWLVDITGYDAMCMQPNSGASGEYAGLLAIKKYHESRGEGHRNVCLI 601

Query: 601 PASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVY 660
           P SAHGTNPASA +AGM++VV ACDK GN+D+ DL+AKA +  +NLSCIMVTYPSTHGVY
Sbjct: 602 PQSAHGTNPASAQLAGMKIVVTACDKQGNVDMEDLKAKAAEVAENLSCIMVTYPSTHGVY 661

Query: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720
           EETI E+CEV+HQ GGQVYLDGANMNAQVG+TSPG IGADVSHLNLHKTF IPHGGGGPG
Sbjct: 662 EETISEICEVIHQHGGQVYLDGANMNAQVGLTSPGSIGADVSHLNLHKTFAIPHGGGGPG 721

Query: 721 MGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKK 780
           MGPIGVKAHLAPFV GH+VV+        GAVSAAP+GSASILPI+WMYI+++G +GL++
Sbjct: 722 MGPIGVKAHLAPFVAGHAVVKHGRESDNNGAVSAAPYGSASILPITWMYIKLLGYQGLRQ 781

Query: 781 ASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDY 840
           ++Q+A+LNANY+  +L   +PVLYTGR+ RVAHECI+D+RPLKE +G++E+DIAKRL DY
Sbjct: 782 STQMALLNANYVMKKLSAHYPVLYTGRNDRVAHECIIDLRPLKEASGVTEMDIAKRLNDY 841

Query: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNA 900
           GFHAPTMSFPVAGTLM+EPTESESK ELDRFI+AM+AIR EI +V+AG WP ++NPL NA
Sbjct: 842 GFHAPTMSFPVAGTLMIEPTESESKAELDRFIEAMVAIRGEIAKVEAGEWPADNNPLHNA 901

Query: 901 PHIQSELV-AEW-AHPYSREVAVFPAGV--ADKYWPTVKRLDDVYGDRNLFCSCVPISEY 956
           PH  ++++ +E+ + PYSRE AVFP     A+K+WPTV R+DDVYGDRNL CSC PI +Y
Sbjct: 902 PHTMADIMDSEFDSRPYSRETAVFPTAAVKANKFWPTVNRIDDVYGDRNLMCSCAPIDDY 961

Query: 957 Q 957
           +
Sbjct: 962 K 962


Lambda     K      H
   0.319    0.134    0.395 

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: 2256
Number of extensions: 82
Number of successful extensions: 7
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: 957
Length of database: 962
Length adjustment: 44
Effective length of query: 913
Effective length of database: 918
Effective search space:   838134
Effective search space used:   838134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate 5210634 Shew_3062 (glycine dehydrogenase (RefSeq))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.21031.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21031.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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