GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Burkholderia phytofirmans PsJN

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate BPHYT_RS19330 BPHYT_RS19330 glycine dehydrogenase (decarboxylating)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5558
         (953 letters)



>FitnessBrowser__BFirm:BPHYT_RS19330
          Length = 978

 Score = 1274 bits (3297), Expect = 0.0
 Identities = 643/955 (67%), Positives = 764/955 (80%), Gaps = 16/955 (1%)

Query: 11  FIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMG---DGQSEADALAS 67
           F  RHIGP A+D+ AMLE LG+ S  AL  +VIP++I+ T  L +G     +SEA+ALA+
Sbjct: 26  FAERHIGPDAADQHAMLEALGFASRAALIDAVIPKTIRRTETLPLGPFTQPKSEAEALAA 85

Query: 68  IKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNF 127
           ++ +A KNQ+F++YIGQGYYN HTP  ILRN+LENPAWYTAYTPYQPEISQGRLEALLNF
Sbjct: 86  LRELADKNQVFRSYIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNF 145

Query: 128 QTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQTLDVLRTR 187
           Q +I DLTGL I+NASLLDEATAAAEAMT  +R+ K K SN FF +    PQT++V+RTR
Sbjct: 146 QQMIVDLTGLAISNASLLDEATAAAEAMTLLQRVGKPK-SNVFFVADDVLPQTIEVVRTR 204

Query: 188 AEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALVAVAADLL 247
           A P+GI+V VG   E ++ + F G LLQYP  NGD+ DYR LTE  H A   V VAADLL
Sbjct: 205 ATPVGIEVKVGPASEAANANAF-GVLLQYPGVNGDVRDYRALTEAIHAAGGHVVVAADLL 263

Query: 248 ALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFG 307
           ALT+LTPPGE+GADVA+G+ QRFGVP+GFGGPHAAY + +D FKR MPGRLVGV+VD  G
Sbjct: 264 ALTVLTPPGEWGADVAVGNTQRFGVPVGFGGPHAAYLAVRDEFKRQMPGRLVGVTVDAQG 323

Query: 308 KPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANRIHHLTAI 367
            PALRLA+QTREQHIRREKATSN+CTAQ LLA +ASMYAVYHGP GL  IA R++ + A+
Sbjct: 324 NPALRLALQTREQHIRREKATSNVCTAQALLAIMASMYAVYHGPHGLKTIALRVNRIAAL 383

Query: 368 LAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGLSLDETTS 427
           LA+G   LG ++  E+FFDTLT  TGA+T AL D A A+RINLR V A ++GLS+DETT+
Sbjct: 384 LAEGAKQLGYTLANETFFDTLTFDTGARTQALLDAATAKRINLRRVSATQVGLSIDETTT 443

Query: 428 QADVEALLRLIGNLMADGKAVPDF----AALAASVQSHIPAELVRQSAILSHPVFNRYHS 483
           + D+  LL +     A    VP      A LAAS  + +PA L R SA L+H VFNR+HS
Sbjct: 444 RHDLADLLAVFAQA-AFTNDVPQVDALDAKLAASNTASVPAALERTSAYLTHHVFNRHHS 502

Query: 484 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 543
           ETE++RYLR L+DKDLALDR+MIPLGSCTMKLNA SEM+PVTW EFG +HPFAPAEQ+ G
Sbjct: 503 ETEMLRYLRSLSDKDLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPFAPAEQTVG 562

Query: 544 YQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 603
           Y+++ D+LE ML AATGY AVSLQPNAGSQGEYAGLL I AYH SRGE  R++CLIP+SA
Sbjct: 563 YREMIDQLEEMLVAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPASA 622

Query: 604 HGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 663
           HGTNPA+A MAGM+VVV ACDA+GNVDIEDL+ KA +H + LAA+MITYPSTHGVFE+ +
Sbjct: 623 HGTNPASAQMAGMQVVVVACDAQGNVDIEDLKKKAGQHADKLAAIMITYPSTHGVFEQNV 682

Query: 664 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 723
           REIC I+H +GGQVY+DGANMNAMVGL APG+FGGDVSHLNLHKTFCIPHGGGGPGVGP+
Sbjct: 683 REICEIVHAHGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPV 742

Query: 724 GVKSHLAPFLPGHASMERKQ-----GAVCAAPFGSASILPITWMYIRMMGGAGLKRASQL 778
            V +HLA FLP   S   ++     GAV  AP+GSASILPI+WMYI MMG   L  A++ 
Sbjct: 743 AVGAHLAQFLPNQISSGYERAPNGIGAVSGAPYGSASILPISWMYIAMMGAKNLTAATET 802

Query: 779 AILNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHA 838
           AILNANY+A++L  HYPVLYSG  GLVAHECILDLRP+K++SGI+VDDVAKRL D+GFHA
Sbjct: 803 AILNANYVAKKLAPHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHA 862

Query: 839 PTMSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTA 898
           PTMSFPV GTLM+EPTESESKEELDRF +AMI IREEIRAVE+G  D++DNPLK+APHTA
Sbjct: 863 PTMSFPVPGTLMVEPTESESKEELDRFIEAMIAIREEIRAVEDGRSDREDNPLKHAPHTA 922

Query: 899 AEIV-GEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESY 952
           A ++  +W H Y+RE A YP+ +LI  KYWPPVGR DNV+GDRNL C+C  I  Y
Sbjct: 923 AVVIANDWKHAYARETAAYPLPTLIAKKYWPPVGRADNVYGDRNLFCSCVPIADY 977


Lambda     K      H
   0.319    0.135    0.398 

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: 2277
Number of extensions: 98
Number of successful extensions: 10
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: 953
Length of database: 978
Length adjustment: 44
Effective length of query: 909
Effective length of database: 934
Effective search space:   849006
Effective search space used:   849006
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 BPHYT_RS19330 BPHYT_RS19330 (glycine dehydrogenase (decarboxylating))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.18243.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18243.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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