Alignments for a candidate for bamH in Methanobacterium veterum MK4

GapMind for catabolism of small carbon sources

Alignments for a candidate for bamH in Methanobacterium veterum MK4

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_084689146.1 EJ01_RS05430 NADH dehydrogenase

Query= uniprot:Q39TW5
         (635 letters)



>NCBI__GCF_000745485.1:WP_084689146.1
          Length = 627

 Score =  585 bits (1508), Expect = e-171
 Identities = 292/627 (46%), Positives = 415/627 (66%), Gaps = 33/627 (5%)

Query: 10  LECARKDIVSRIDPTKPCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCP 69
           ++ A+ +  S      P I + +     ++GAA V +  + ELE +    E+     GC 
Sbjct: 7   VKTAKNEYESLYKGEDPLILIGSATCGKSAGAALVKSVIQEELEKNNANAEIIE--VGCI 64

Query: 70  GFCERGPIVMIYPEG-----------------ICYLKVKPEDVPEIVSHTIKEKKVVDRL 112
           G C   PI+ I+ +G                 I    VK + +PE    TI E K+    
Sbjct: 65  GLCYAEPIITIFKQGNPGIFYGNVTKKTAQEIIRSYIVKDDPLPEYALGTIGEGKIEGIP 124

Query: 113 LYEDPATGTRALRESDIPFYKNQQRNILSENLRLDSKSMDDYLAIGGYSALSKVLFQMTP 172
           L+ D    T+AL        K Q R IL     +D K+++ Y+A  GYS     + +M P
Sbjct: 125 LFFD----TKAL--------KPQVRRILRNCGIIDPKNINHYIANDGYSGFMDAI-KMAP 171

Query: 173 EDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGN 232
           E+V+ +IK+S LRGRGG GFP W KW+  R++    +Y+I NADEGDPGAFM+R+L+E +
Sbjct: 172 EEVIEKIKESGLRGRGGAGFPTWMKWQFCRDSGGETRYLICNADEGDPGAFMNRSLLESD 231

Query: 233 PHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILGSGFDFT 292
           PHS+LEG++I  Y +GA + +IY R EYPLA++++  AI+Q  E GF+G++I GSGF+F 
Sbjct: 232 PHSVLEGILIAGYVIGAKKAYIYCRAEYPLALDHLKHAIKQMREYGFLGENICGSGFNFD 291

Query: 293 VKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQI 352
           +++  GAGAFVCGE +AL+ ++EG+ G PR +       G++  P+V+NNVET A+V  I
Sbjct: 292 IEIKEGAGAFVCGEETALIASVEGKRGTPRTRPPFPTTSGLFGKPTVINNVETLASVALI 351

Query: 353 ITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFK 412
           + K  D F  +GT  S GTK FSLVG+I   GL+EVP+G TLR++I  +GGGIPGGKKFK
Sbjct: 352 MQKNPDKFAEFGTDSSKGTKTFSLVGEIERPGLIEVPLGTTLREVIFDIGGGIPGGKKFK 411

Query: 413 AVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKD 472
           AVQ GGPSGGC+PE+ +D P+D+D LT AG++MGSGG+++MDE TCMV+++RYF++F + 
Sbjct: 412 AVQIGGPSGGCLPESFIDTPIDYDSLTMAGAIMGSGGLVIMDESTCMVEVSRYFLEFSQR 471

Query: 473 ESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELAES-TGAALCALGKSAPNPVL 531
           ESCGKC PCR G +QML +LT IT GKGK  D++LL++LAE     +LC LG++ PNPVL
Sbjct: 472 ESCGKCVPCRLGAKQMLDILTDITEGKGKPEDVQLLKDLAEGIKKGSLCGLGQNTPNPVL 531

Query: 532 STIRYFRDEYEAHIREKKCPALSCKEMIAFHIDPEKCKACGSCFRQCPAEAIQGGKKLIH 591
           +T+++F +EY+AHI ++ CPAL+CKE I++HI  E+C  C  CF+ CP +AI G KK  H
Sbjct: 532 TTLKFFENEYDAHINDQLCPALACKEFISYHIITEECNGCRLCFKSCPVDAISGEKKEPH 591

Query: 592 IIDQEKCTKCGTCLDVCPSRFGAVRKI 618
           +IDQEKC KCGTC+++C  ++ A+  I
Sbjct: 592 VIDQEKCIKCGTCIELCSGKYDAMECI 618


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: 1268
Number of extensions: 63
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 635
Length of database: 627
Length adjustment: 38
Effective length of query: 597
Effective length of database: 589
Effective search space:   351633
Effective search space used:   351633
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 2024 update 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