GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Acidovorax sp. GW101-3H11

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Ac3H11_1447 NADH-ubiquinone oxidoreductase chain F (EC 1.6.5.3)

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1447
          Length = 452

 Score =  317 bits (811), Expect = 9e-91
 Identities = 168/412 (40%), Positives = 249/412 (60%), Gaps = 8/412 (1%)

Query: 150 SMDDYLAIGGYSALSKVLFQ-----MTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNA 204
           S+ DY A GGY+AL K+L       +T + V+  +K+S LRGRGG GFP   KW     +
Sbjct: 39  SIKDYEARGGYAALRKILGTDGGEPLTQDQVIATVKESGLRGRGGAGFPTGLKWSFMPRS 98

Query: 205 PDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAV 264
               KY++ N+DEG+PG   DR +++ NPH ++EG+II AYA+G   G+ Y+  E     
Sbjct: 99  FPGQKYLVCNSDEGEPGTCKDRDILQFNPHIVIEGMIIAAYAMGISVGYNYIHGEIFQTY 158

Query: 265 ENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPK 324
           +    A+ +A   G++G  ILGS F F +    G GA++CGE +AL+ +LEG+ G+PR K
Sbjct: 159 DRFEAALEEARAAGYLGDKILGSNFSFQLHAAHGFGAYICGEETALLESLEGKKGQPRFK 218

Query: 325 YIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTG 384
               A  G++  P+ +NN ET+A V  II  G   +   G   + GTKIFS+ G +   G
Sbjct: 219 PPFPASFGLYGKPTTINNTETFAAVPWIIRNGGAAYLECGKPNNGGTKIFSVSGDVEKPG 278

Query: 385 LVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAML-DLPVDFDELTKAGS 443
             EVP+G     ++ ++ GG+  G++ KAV  GG S   +P +++ +  +D+D + KAGS
Sbjct: 279 NYEVPLGTPFAKLL-ELAGGVRKGRQLKAVIPGGSSAPVLPASIIMECTMDYDSIAKAGS 337

Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEG 503
           M+GSG +IVMD+   MV+       F   ESCG+CTPCREG   M  V+ RI  G+G++G
Sbjct: 338 MLGSGAVIVMDDSRSMVESLLRLSYFYSHESCGQCTPCREGTGWMWRVIDRIQHGQGRDG 397

Query: 504 DIELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCPALS 554
           D+ LL  +A++  G  +CALG +A  PV + I++FR E+EA IR++K P  S
Sbjct: 398 DLNLLNSVADNIQGRTICALGDAAAMPVRAMIKHFRPEFEALIRQEKTPQAS 449


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: 758
Number of extensions: 38
Number of successful extensions: 4
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: 452
Length adjustment: 35
Effective length of query: 600
Effective length of database: 417
Effective search space:   250200
Effective search space used:   250200
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.

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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