GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamH in Burkholderia phytofirmans PsJN

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate BPHYT_RS06650 BPHYT_RS06650 NADH dehydrogenase

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS06650 BPHYT_RS06650 NADH
           dehydrogenase
          Length = 442

 Score =  327 bits (839), Expect = 5e-94
 Identities = 170/415 (40%), Positives = 252/415 (60%), Gaps = 4/415 (0%)

Query: 139 ILSENLRLDSKSMDDYLAIGGYSALSKVLFQ-MTPEDVMGEIKKSNLRGRGGGGFPAWRK 197
           ++   L  D+  ++DY+A GGY+ L ++L + + PE V+ ++K S LRGRGG GFP   K
Sbjct: 12  LILAGLNGDNWHLEDYVARGGYAQLRRILEEKIPPEQVIADVKASGLRGRGGAGFPTGLK 71

Query: 198 WEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVR 257
           W          KY++ N+DEG+PG F DR ++  NPHS++EG+ IGAYA+G   G+ Y+ 
Sbjct: 72  WSFMPRQFPGQKYLVCNSDEGEPGTFKDRDILRFNPHSLIEGMAIGAYAMGITVGYNYIH 131

Query: 258 QEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGR 317
            E     +    A+ +A   GF+G++I+GSGF F +  H G GA++CGE +AL+ +LEG+
Sbjct: 132 GEIWEVYKRFEQALDEARRAGFLGENIMGSGFSFELHAHHGYGAYICGEETALLESLEGK 191

Query: 318 AGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLV 377
            G+PR K    A  GV+  P+ +NN ET+A V  ++  G   +   G   + GTKIFS+ 
Sbjct: 192 KGQPRFKPPFPASFGVYGKPTTINNTETFAAVPFLLAIGPQNYLEIGKPNNGGTKIFSVA 251

Query: 378 GKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIP-EAMLDLPVDFD 436
           G +   G  E+P+G     ++ ++ GG+ G KK KAV  GG S   IP + M+   +D+D
Sbjct: 252 GDVERPGNYEIPLGTPFSTLM-ELAGGMRGVKKIKAVIPGGSSAPVIPGDIMMQTDMDYD 310

Query: 437 ELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRIT 496
            + KAGSM+GSG +IVMDE  CMV        F  +ESCG+CTPCREG   +  V+ RI 
Sbjct: 311 SIAKAGSMLGSGAVIVMDETRCMVRSLLRLSYFYYEESCGQCTPCREGTGWLYRVVHRIE 370

Query: 497 VGKGKEGDIELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKC 550
            G G+  D++LL  +AE+  G  +CALG +A  PV   ++++ DE+E H+  K C
Sbjct: 371 HGLGRPEDLDLLNSVAENIMGRTICALGDAAAMPVRGMLKHYWDEFEYHVAHKHC 425


Lambda     K      H
   0.319    0.138    0.420 

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: 763
Number of extensions: 38
Number of successful extensions: 6
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: 635
Length of database: 442
Length adjustment: 35
Effective length of query: 600
Effective length of database: 407
Effective search space:   244200
Effective search space used:   244200
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: 52 (24.6 bits)

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

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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