Alignments for a candidate for fumD in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Dechlorosoma suillum PS

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate Dsui_2001 Dsui_2001 hydro-lyase, Fe-S type, tartrate/fumarate subfamily,hydro-lyase family enzyme, Fe-S type, tartrate/fumarate subfamily

Query= BRENDA::Q141Z6
         (520 letters)



>FitnessBrowser__PS:Dsui_2001
          Length = 510

 Score =  786 bits (2029), Expect = 0.0
 Identities = 386/508 (75%), Positives = 443/508 (87%), Gaps = 4/508 (0%)

Query: 14  MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73
           M+ I+QEDLIQSIAD+ QYISYYHPLDYI+ALG AYE E+SPAAKDAIAQILTNSRM AE
Sbjct: 1   MSSIRQEDLIQSIADAFQYISYYHPLDYIKALGEAYEREESPAAKDAIAQILTNSRMAAE 60

Query: 74  GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133
           G RPICQDTGI  VF+KVGM+VRWD ATM + +M+NEGVRR Y NPDN LRAS+++ P G
Sbjct: 61  GHRPICQDTGIGMVFLKVGMNVRWDDATMSLQEMVNEGVRRAYANPDNPLRASVLADPAG 120

Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193
            RKNTKDNTPAV+H+EIVPG+ V+V  AAKGGGSE KSKFAMLNPSD +VDW+LK +P M
Sbjct: 121 ARKNTKDNTPAVVHFEIVPGDHVEVICAAKGGGSEAKSKFAMLNPSDDLVDWVLKKIPEM 180

Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDI---QDVIARGPK-DWIEELRVELHE 249
           GAGWCPPG++GIGIGGT EKAM++AKES+M P+DI   QD    G K    EELR+EL+E
Sbjct: 181 GAGWCPPGIIGIGIGGTPEKAMLLAKESIMAPVDIHDLQDKAKSGAKLTRAEELRLELYE 240

Query: 250 KVNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLE 309
           KVNALG+GAQGLGGL TVLDVK++  P HAA+ PVA++PNCAATRH HF LDGSG A++E
Sbjct: 241 KVNALGVGAQGLGGLTTVLDVKVLDYPCHAANLPVALVPNCAATRHCHFHLDGSGPAKIE 300

Query: 310 APSLDAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIAD 369
            P L+ WP V W PD + + +V+L+TLT EEVA+W PGQ LLL+GKMLTGRDAAHKRIAD
Sbjct: 301 PPKLEDWPAVTWTPDLKAATQVNLDTLTKEEVASWKPGQKLLLNGKMLTGRDAAHKRIAD 360

Query: 370 MLAKGEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIG 429
           MLAKGEKLPVDFTNRVIYYVGPVDPVRDE VGPAGPTTATRMDKFT MML +TGLISMIG
Sbjct: 361 MLAKGEKLPVDFTNRVIYYVGPVDPVRDEVVGPAGPTTATRMDKFTRMMLEKTGLISMIG 420

Query: 430 KAERGPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPV 489
           K+ERGPVAIEAI+ +K+AYLMAVGGAAYLV+KAI+SAKV+ F DLGMEAIYEF+VQ+MPV
Sbjct: 421 KSERGPVAIEAIKDNKSAYLMAVGGAAYLVAKAIKSAKVVGFADLGMEAIYEFEVQNMPV 480

Query: 490 TVAVDSNGTSVHQTGPKEWQARIGKIPV 517
           TVAVDS+GTSVH+TGPKEWQ +IGKIPV
Sbjct: 481 TVAVDSSGTSVHETGPKEWQVKIGKIPV 508


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: 928
Number of extensions: 30
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: 510
Length adjustment: 35
Effective length of query: 485
Effective length of database: 475
Effective search space:   230375
Effective search space used:   230375
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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 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