GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Xanthobacter autotrophicus Py2

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_012115455.1 XAUT_RS17550 NADH-quinone oxidoreductase subunit NuoF

Query= uniprot:Q39TW5
         (635 letters)



>NCBI__GCF_000017645.1:WP_012115455.1
          Length = 520

 Score =  327 bits (838), Expect = 8e-94
 Identities = 185/519 (35%), Positives = 282/519 (54%), Gaps = 16/519 (3%)

Query: 26  PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG- 84
           P I V   A  +A GA  V    +  L   G+T ++   G+   G     P++ +  E  
Sbjct: 4   PRIFVPNDATAVACGADRVARKLEAGLLARGITADITRNGSR--GLFWLEPLIEVETERG 61

Query: 85  -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSEN 143
            I Y  VKP D+ +++   I      D  L              +IP+ K Q R   +  
Sbjct: 62  RIGYGPVKPSDIEDLLHAGILHG--ADHPLCVGLV--------DEIPYLKKQTRLTFARI 111

Query: 144 LRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRN 203
             +D  S+ DY A GGY  L + +  + P   + E+ +S LRGRGG GFP   KW     
Sbjct: 112 GIIDPLSLTDYKAHGGYRGLERAI-TLGPSATVEEVVESGLRGRGGAGFPTGIKWRTVAA 170

Query: 204 APDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLA 263
           AP   +Y++ NADEGD G F DR ++E +P  ++EG+ I   AVGA +G++Y R EYPLA
Sbjct: 171 APADQRYIVCNADEGDSGTFADRLIMEADPFCLIEGMTIAGLAVGATKGYVYSRSEYPLA 230

Query: 264 VENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRP 323
              +  AI +A E G +G +ILGSG  F +++ MGAGA+VCGE +AL+ +LEG+ G  R 
Sbjct: 231 FVVMEKAIEKAREAGLLGDNILGSGLSFDMEMRMGAGAYVCGEETALLESLEGKRGLVRA 290

Query: 324 KYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNT 383
           K    A KG++  P+V+NN+ + A V  I+ KG  ++  +G   S GT    + G I   
Sbjct: 291 KPPLPAHKGLFQKPTVINNLVSLATVPVILDKGGKYYRDFGMGRSRGTMPIQIAGNIKFG 350

Query: 384 GLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGS 443
           GL E   G+ L +++  +GGG   G+  KAVQ GGP G  +P    D P D++      +
Sbjct: 351 GLFETAFGIPLGELVYDIGGGTASGRPVKAVQAGGPLGAYLPTHQFDTPFDYEAFAAKDA 410

Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEG 503
           ++G GG++V D+   + D+A++ ++F   ESCGKCTPCR G  + +  + ++  G+ +E 
Sbjct: 411 LIGHGGLVVFDDTADLADMAKFAMEFCAHESCGKCTPCRIGSTRGVETIDKVIAGEKREQ 470

Query: 504 DIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541
           ++ LL +L  +    +LCALG   P PVLS + +F +++
Sbjct: 471 NLALLTDLCHTMKLGSLCALGGFTPYPVLSALNHFPEDF 509


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: 867
Number of extensions: 48
Number of successful extensions: 3
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: 520
Length adjustment: 36
Effective length of query: 599
Effective length of database: 484
Effective search space:   289916
Effective search space used:   289916
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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