GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Pseudomonas fluorescens FW300-N1B4

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate Pf1N1B4_2236 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)

Query= CharProtDB::CH_003480
         (957 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236
          Length = 957

 Score = 1261 bits (3264), Expect = 0.0
 Identities = 631/957 (65%), Positives = 754/957 (78%), Gaps = 8/957 (0%)

Query: 4   TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
           +LSQL +   F+ RH+GPDAA+QQ ML+++G  S   L  Q VP  I+L  P  +     
Sbjct: 6   SLSQLRDPNTFLRRHLGPDAAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRPLDLPPALD 65

Query: 64  EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
           E AALA+L+  A +N+ +TS IGMGY     P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66  EEAALAKLRGYAEQNQIWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGR 125

Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
           LEALLNFQQ+T+DLTGL++A+ASLLDEATAAAEAMA+AKRV+K ++ N FFV  + HPQT
Sbjct: 126 LEALLNFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSRS-NLFFVDENCHPQT 184

Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
           + VVRTRAE FGFE+I+D    +  HQ VFG LLQ   T GE+ D   LI  L +++ +V
Sbjct: 185 ISVVRTRAEGFGFELIIDAVDNLKQHQ-VFGALLQYPDTHGEVRDLRPLIDHLHAQQALV 243

Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
            VA D+++L+LLT PG+ GAD+VFGS+QRFGVPMGYGGPHAAFFA++DEYKR++PGRIIG
Sbjct: 244 CVATDLLSLLLLTPPGELGADVVFGSSQRFGVPMGYGGPHAAFFASRDEYKRAIPGRIIG 303

Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
           VSKDA GN ALRMA+QTREQHIRREKANSNICT+QVLLANIAS YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHGPEGLKRIAQR 363

Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVAD-KAGVLTRAEAAEINLRSDILNAVGI 422
           +HRLT ILAAGL++ G+   + ++FDTL +EV   +  ++  A+AA+INLR      +G+
Sbjct: 364 VHRLTCILAAGLERHGITRLNQNFFDTLTLEVGGTQTAIIESAQAAQINLRILGRGQLGL 423

Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
           +LDET     V +LF+V LG +HGL++D LD +       I   + R    L HPVFN +
Sbjct: 424 SLDETCDETTVAKLFDVFLGADHGLNVDDLDAETLVSG--IPAGLQRSTSYLRHPVFNAH 481

Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
           HSETEM+RY+  LE KDLALNQ+MIPLGSCTMKLNA +EMIPITWP+FA LHPF P EQ 
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPQFANLHPFVPKEQV 541

Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
            GY  MIA+L  WL  +TG+DA+CMQPNSGAQGEYAGLLAIR YHESR++G RDICLIP+
Sbjct: 542 VGYSLMIAELERWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRHQGARDICLIPS 601

Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
           SAHGTNPASA MAGM+VV+V CD+ GN+DL DL+ KA +AGD L+C+M TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMRVVIVECDEGGNVDLDDLKEKATEAGDKLACLMATYPSTHGVYEE 661

Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
            I E+CEV+H  GGQVY+DGAN+NAQVG+  P  IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721

Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
           PIGV+AHLAPFV  H VV I+G L   GAVSAAP+GSASILPISWMYI MMG + L  AS
Sbjct: 722 PIGVRAHLAPFVANHPVVPIDGPLPENGAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780

Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
           +VAIL ANY+A  L  AFPVLYTGR+ RVAHECILD+RPLK +TGISE D+AKRL+DYGF
Sbjct: 781 EVAILAANYLAQHLAGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGF 840

Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
           HAPTMSFPV GTLMVEPTESESK ELDRFI AML+IRAEI +V+ G WP EDNPL  +PH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFIGAMLSIRAEITEVQNGNWPAEDNPLKRSPH 900

Query: 903 IQSELVAEWAHPYSREVAVFPAG--VADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
             +++   W  PYS E AV P     A KYWP V R+D+VYGDRNLFC+CVP+ EY+
Sbjct: 901 TLADITGVWERPYSIERAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCACVPVDEYR 957


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: 2345
Number of extensions: 84
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: 957
Length adjustment: 44
Effective length of query: 913
Effective length of database: 913
Effective search space:   833569
Effective search space used:   833569
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 Pf1N1B4_2236 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.4057.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4057.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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