GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Rhizobium etli CFN 42

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_011426948.1 RHE_RS19125 NADH-quinone oxidoreductase subunit NuoF

Query= uniprot:Q39TW5
         (635 letters)



>NCBI__GCF_000092045.1:WP_011426948.1
          Length = 420

 Score =  383 bits (983), Expect = e-110
 Identities = 187/402 (46%), Positives = 262/402 (65%), Gaps = 2/402 (0%)

Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKY 210
           +  Y A GGY AL KVL + TP++V+  +K+SNLRGRGG GF    KW          KY
Sbjct: 18  LSTYEAGGGYQALVKVLREYTPDEVVELVKRSNLRGRGGAGFLTGMKWSFVPKQSSKPKY 77

Query: 211 VIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLA 270
           +  NADEG+PG F DR L+E +PH ++EGL + AYA+GA   ++Y+R EY  A+  +  A
Sbjct: 78  LCCNADEGEPGTFKDRILMERDPHQLIEGLAVSAYAIGAKTAYVYIRGEYVTAIRRLEQA 137

Query: 271 IRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAV 330
           I +A  +G++G  ILGS F+FTV +H GAGA++CGE +A++ +LEGR  +PR K    AV
Sbjct: 138 IAEAHAKGYLGSRILGSDFNFTVHIHCGAGAYICGEETAMLESLEGRRAQPRLKPPFPAV 197

Query: 331 KGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPM 390
            G++  P+V+NNVET A V  I+ +G+DWF   G   S G K++ + G++   GL E+PM
Sbjct: 198 AGLYASPTVINNVETLACVPHIVVRGSDWFRDIGPEKSPGPKLYCVSGQVRKPGLYELPM 257

Query: 391 GVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGM 450
           G+ LR+++   GG  P G++ KAV  GG S   IPE  LD+ +DFD L  AGSM+GS G+
Sbjct: 258 GIPLRELVDHAGGP-PPGRRIKAVIPGGVSAPVIPEHGLDVGMDFDSLAAAGSMLGSAGV 316

Query: 451 IVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEE 510
           IV+D  TCMV +A   I+F   ESCGKCTPCREG+  ++ +L RI  G G  GD+E L+ 
Sbjct: 317 IVIDNSTCMVKVATRIIEFFHHESCGKCTPCREGLNWVVKILRRIEAGDGAPGDLEQLDM 376

Query: 511 LAEST-GAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCP 551
           L +   G   CALG  A   + + +++FR+E+ AHI E++CP
Sbjct: 377 LCKGIFGNTFCALGDGAAMGLRAALKHFREEFVAHIEERRCP 418


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: 764
Number of extensions: 46
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: 420
Length adjustment: 35
Effective length of query: 600
Effective length of database: 385
Effective search space:   231000
Effective search space used:   231000
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 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