Alignments for a candidate for fumD in Caldicellulosiruptor hydrothermalis 108

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Caldicellulosiruptor hydrothermalis 108

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_013404426.1 CALHY_RS13140 fumarate hydratase

Query= BRENDA::Q141Z6
         (520 letters)



>NCBI__GCF_000166355.1:WP_013404426.1
          Length = 278

 Score =  179 bits (455), Expect = 9e-50
 Identities = 109/285 (38%), Positives = 160/285 (56%), Gaps = 15/285 (5%)

Query: 14  MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73
           M ++  E + Q + +++       P D   +L +AY  E+   AK  +  ++ N  +  +
Sbjct: 1   MRIVPAEIIEQKVYEAINQAVCILPDDVKDSLHKAYASEEG-IAKYTLENLIKNIDLAQQ 59

Query: 74  GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133
             RP+CQDTG    FV++G DV  +G+   + D IN  V R Y   D  LR S+V  P  
Sbjct: 60  KMRPVCQDTGAAVFFVEIGEDVFIEGS---LKDAINRAVSRAYT--DFYLRKSMVKSPIE 114

Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVD---WILKTV 190
            R+NT DNTPA+IH ++  G+ + +    KG GSENKS   ML P+D I     ++++TV
Sbjct: 115 -RENTLDNTPAIIHIDMAKGDKITIHFMPKGFGSENKSTICMLTPADGIEGIEKFVVETV 173

Query: 191 PTMGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEK 250
              G+  CPP ++G+GIGGT E A +++K++L+     + V  R P+ +I EL   L EK
Sbjct: 174 KKAGSDPCPPILVGVGIGGTFELAALLSKKALL-----RKVGQRHPRKYIAELEERLLEK 228

Query: 251 VNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRH 295
           +N+LGIG +G GG  T LDV I   PTH A  PVA+   C   RH
Sbjct: 229 INSLGIGPEGFGGKTTALDVFIEEFPTHIAGLPVAVNICCHVARH 273


Lambda     K      H
   0.316    0.133    0.392 

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: 337
Number of extensions: 13
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: 520
Length of database: 278
Length adjustment: 30
Effective length of query: 490
Effective length of database: 248
Effective search space:   121520
Effective search space used:   121520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_013404010.1 CALHY_RS10935 fumarate hydratase

Query= BRENDA::Q141Z6
         (520 letters)



>NCBI__GCF_000166355.1:WP_013404010.1
          Length = 185

 Score =  170 bits (431), Expect = 3e-47
 Identities = 81/179 (45%), Positives = 116/179 (64%), Gaps = 1/179 (0%)

Query: 330 RVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKGEKLPVDFTNRVIYYV 389
           R+ +    PEE+     GQ +L+ GK+   RDAAHKR+ +M+ KG K+P+DF N  IYY+
Sbjct: 3   RIYVPVQNPEEIQKLKCGQEVLVCGKLFVARDAAHKRLFEMIQKGSKIPIDFKNGAIYYM 62

Query: 390 GPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAERGPVAIEAIRKHKAAYL 449
           GP      E +GP GPTTA RMD FT MML + G+  +IGK +R     EAI+KH + YL
Sbjct: 63  GPCPEKPCEVIGPCGPTTAGRMDVFTPMML-ELGIKVLIGKGKRNEAVKEAIKKHGSIYL 121

Query: 450 MAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAVDSNGTSVHQTGPKEW 508
              GGAA L+   ++S +++ FEDLG EAI E +V+D+P  VA+D  G  +++ GP+++
Sbjct: 122 ATFGGAAVLIQSCVKSQRIVMFEDLGAEAIREIEVEDLPCIVAIDGQGEDIYEVGPRKY 180


Lambda     K      H
   0.316    0.133    0.392 

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: 250
Number of extensions: 11
Number of successful extensions: 2
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: 520
Length of database: 185
Length adjustment: 27
Effective length of query: 493
Effective length of database: 158
Effective search space:    77894
Effective search space used:    77894
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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