Alignments for a candidate for bamH in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for bamH in Cupriavidus basilensis 4G11

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate RR42_RS31315 RR42_RS31315 NADH-quinone oxidoreductase subunit F

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__Cup4G11:RR42_RS31315
          Length = 569

 Score =  254 bits (649), Expect = 7e-72
 Identities = 165/520 (31%), Positives = 253/520 (48%), Gaps = 60/520 (11%)

Query: 23  PTKPCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYP 82
           P    + VC G  C   G  +++A     L      +EV      C G CER P  ++  
Sbjct: 106 PAAVTVRVCEGIACELGGGRDLLARLPALLG-----SEVKVVAAPCIGRCERAPAALVGQ 160

Query: 83  EGICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSE 142
             + +   +          TI +  V  R ++  P        E+ + +           
Sbjct: 161 NPVDFASAQ----------TIADT-VAARAVHHAP--------EAHLGY----------- 190

Query: 143 NLRLDSKSMDDYLAIGGYSALSKVLF-QMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEES 201
                    DDY A GGY  L  V   +   E ++  ++ S LRG GG GFP  RKW   
Sbjct: 191 ---------DDYRAQGGYQLLRAVASGEHDSESLLRTMEDSGLRGLGGAGFPTGRKWRIV 241

Query: 202 RNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYP 261
              P P + + VN DEG+PG F DR  +E +PH  LEG++I A        +IY+R EY 
Sbjct: 242 MAEPAP-RLMAVNLDEGEPGTFKDRVYLERDPHRFLEGMLIAAAVTQVSAIYIYLRDEYA 300

Query: 262 LAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEP 321
                +  A+R+      +  D+        +++  GAGA++CGE SA++ ++EG+ G P
Sbjct: 301 GCRAVLGQALRRLQAEPPI-PDMP------QIQLRRGAGAYICGEESAMIESIEGKRGMP 353

Query: 322 RPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKIT 381
           R +  + A  G++  P++ +N ET   V +I+ KGA WF + G  G  G + FS+ G++ 
Sbjct: 354 RLRPPYVAQVGLFGRPTLEHNFETLYWVREILEKGAGWFAAQGRHGRHGLRSFSVSGRVK 413

Query: 382 NTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKA 441
             G+   P G+T+ ++I +  GG+  G  F     GG SGG +P ++ D+P+DFD L   
Sbjct: 414 LPGVHVAPAGITVSELIEEYCGGMQDGHCFYGYLPGGASGGILPASLGDIPLDFDTLQPY 473

Query: 442 GSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGK 501
           G  +GS  ++V  E    V +AR  + F K ESCG+CTPCR G  + L V+ +       
Sbjct: 474 GCFIGSAAIVVFSEQDSAVAVARNLMHFFKHESCGQCTPCRVGTAKALDVIAQ------P 527

Query: 502 EGDIELLEEL-AESTGAALCALGKSAPNPVLSTIRYFRDE 540
           + D+  L +L A    A++C LG++APNPV   I+YF  E
Sbjct: 528 KWDLAALADLSAVMRDASICGLGQAAPNPVDCVIKYFPQE 567


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: 872
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 635
Length of database: 569
Length adjustment: 37
Effective length of query: 598
Effective length of database: 532
Effective search space:   318136
Effective search space used:   318136
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources