GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Snodgrassella alvi wkB2

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_025329713.1 SALWKB2_RS00315 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_000600005.1:WP_025329713.1
          Length = 792

 Score =  960 bits (2481), Expect = 0.0
 Identities = 459/800 (57%), Positives = 590/800 (73%), Gaps = 18/800 (2%)

Query: 3   KNSSSFSVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSA 62
           K  +SFS+ R +T++   LT  ++LIGGIWL  +GGS +Y I    + L   L   + S+
Sbjct: 2   KAYTSFSLARIMTLIVLWLTVIYLLIGGIWLIWLGGSAFYAIIALILCLFTTLYHYQRSS 61

Query: 63  ALVVYALLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGA 122
            L +YA+ L  TL WG+WE GTDFWALAPR D+L +FG+WL+ P+  R +     G L  
Sbjct: 62  CLWLYAITLFITLIWGLWESGTDFWALAPRFDLLFLFGLWLLTPWPTRHISASRSGKL-I 120

Query: 123 MGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRF 182
           + +AL+A  +V+ YS+ +DPQ +NG +      AP A   + +A  DWPAY R Q GTR+
Sbjct: 121 ITLALIAILSVMFYSISHDPQQINGTI-TRLQPAPAADD-NGVAAEDWPAYGRTQGGTRY 178

Query: 183 SPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALD 242
           SPL QIN  NVK+L+VAW ++TGD K  +D  E T+E+TPIKI   L++CTPHQ L ALD
Sbjct: 179 SPLTQINTANVKQLKVAWTYRTGDFKTTNDSAETTNELTPIKIGKKLFICTPHQFLDALD 238

Query: 243 AATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRL 302
           A TGK+ W+FDP L++N TFQH+TCRGVSY++   A  +  T  A+C +++ LPVNDGRL
Sbjct: 239 ATTGKRLWRFDPELRSNRTFQHLTCRGVSYYDATTAHSSETTASAICPQKVLLPVNDGRL 298

Query: 303 FALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTR 362
            A++A+TG++CP FG+NGE++LQ K P    G Y PTSPPV+T +TI++ G+VTDN ST+
Sbjct: 299 IAVNAQTGQKCPDFGHNGEINLQAKMPYAFLGGYNPTSPPVVTPSTIIIGGSVTDNLSTK 358

Query: 363 EPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLP 422
           EPSG IRG+DVN G+L WVFD GA++PNA+P ++  F  NSPN+WAP  YD + +IVY+P
Sbjct: 359 EPSGVIRGYDVNNGQLKWVFDTGAENPNAMPGEKTNFVHNSPNAWAPLAYDQQRNIVYIP 418

Query: 423 MGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADIT 482
            GV+TPDIWGG+R   +ERYA+S++ALNA+TGKL+W +QT HHDLWDMD+P+QP+L DIT
Sbjct: 419 TGVSTPDIWGGHRNKLKERYANSLVALNASTGKLLWHFQTTHHDLWDMDVPAQPSLMDIT 478

Query: 483 DKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQ-----GAAKGDHVSATQPYS 537
              G  +  IY   KTGNIFVL+R TG+ +VP  E  VPQ        +G+H +ATQP+S
Sbjct: 479 IPSGKRIAAIYVLTKTGNIFVLNRETGQPIVPVTEQSVPQTLKHGKPTQGEHYAATQPFS 538

Query: 538 ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWG 597
            L+  PK  LTDKDMWGATM+DQL+CR+ FKRL Y G +TPPSE GTLVFPGNLG+FEWG
Sbjct: 539 ALSLMPKDKLTDKDMWGATMFDQLLCRIQFKRLNYNGIYTPPSENGTLVFPGNLGVFEWG 598

Query: 598 GISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVE 657
           GISV+  RQIA+ NP+ LPFVS+LIP  P   ++       G+GTE GIQP YG PYGVE
Sbjct: 599 GISVNQDRQIALMNPIGLPFVSRLIPANPDRAQQKQ-----GAGTENGIQPMYGAPYGVE 653

Query: 658 LNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP----VPLPFKMGMPML 713
           ++PFLSP GLPCKQPAWG+V+ VDL+TN+VVWK+RIGT+RDS P    +P P K+G+P L
Sbjct: 654 ISPFLSPIGLPCKQPAWGFVAGVDLQTNQVVWKKRIGTIRDSLPKLFELP-PLKIGVPGL 712

Query: 714 GGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAA 773
           GG ++TAG + F+ AT DNYLRA+ T  G+LLWQ RLPAGGQATPMTY VNGKQYVV  A
Sbjct: 713 GGSISTAGNIMFVSATQDNYLRAYDTSNGDLLWQTRLPAGGQATPMTYAVNGKQYVVQMA 772

Query: 774 GGHGSFGTKLGDYVIAYALP 793
           GGH SFGTK+GDY+IAY LP
Sbjct: 773 GGHSSFGTKMGDYLIAYTLP 792


Lambda     K      H
   0.319    0.137    0.433 

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: 2315
Number of extensions: 133
Number of successful extensions: 16
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: 796
Length of database: 792
Length adjustment: 41
Effective length of query: 755
Effective length of database: 751
Effective search space:   567005
Effective search space used:   567005
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory