Alignments for a candidate for fumD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Pseudomonas stutzeri RCH2

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate GFF3134 Psest_3193 hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region/hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region

Query= BRENDA::Q141Z6
         (520 letters)



>FitnessBrowser__psRCH2:GFF3134
          Length = 507

 Score =  766 bits (1977), Expect = 0.0
 Identities = 376/499 (75%), Positives = 432/499 (86%), Gaps = 1/499 (0%)

Query: 14  MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73
           MTVIKQ+DLIQS+AD+LQ+ISYYHP+D+IQA+  AY  E+SPAA+D++AQIL NSRMCA 
Sbjct: 1   MTVIKQDDLIQSVADALQFISYYHPVDFIQAMHEAYLREESPAARDSMAQILINSRMCAT 60

Query: 74  GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133
           G RPICQDTGIVTVFV+VGMDVRWDGATM + DMINEGVRR Y  P+NVLRASI++ P G
Sbjct: 61  GHRPICQDTGIVTVFVRVGMDVRWDGATMSLDDMINEGVRRAYNLPENVLRASILADPAG 120

Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193
            RKNTKDNTPAVIHY IVPG+ V+V VAAKGGGSENKSK AMLNPSDSIVDW+LKTVPTM
Sbjct: 121 SRKNTKDNTPAVIHYSIVPGDKVEVDVAAKGGGSENKSKMAMLNPSDSIVDWVLKTVPTM 180

Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 253
           GAGWCPPGMLGIGIGGTAEKA VMAKE LMDPIDI ++ ARGP++ IEE+R+EL +KVN 
Sbjct: 181 GAGWCPPGMLGIGIGGTAEKAAVMAKEVLMDPIDIHELKARGPQNRIEEMRLELFDKVNQ 240

Query: 254 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSL 313
           LGIGAQGLGGL TVLDVKIM  PTHAAS PV +IPNCAATRHAHF LDGSG A L  P L
Sbjct: 241 LGIGAQGLGGLTTVLDVKIMDYPTHAASLPVCMIPNCAATRHAHFVLDGSGPAELTPPPL 300

Query: 314 DAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAK 373
           DA+P++ W+     ++RV+L+T+TPEEV +W PG+T+LL+GKMLTGRDAAHKR+ DML K
Sbjct: 301 DAYPEIVWEAG-PSARRVNLDTITPEEVQSWKPGETILLNGKMLTGRDAAHKRMVDMLNK 359

Query: 374 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433
           GE+LPVD   R IYYVGPVDPV DE VGPAGPTTATRMDKFT  +L  TGL+ MIGK+ER
Sbjct: 360 GEELPVDLKGRFIYYVGPVDPVGDEVVGPAGPTTATRMDKFTRQILESTGLLGMIGKSER 419

Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493
           GP+AIEAI+ +KA YLMAVGGAAYLV++AI+ +KVLAF +LGMEAIYEF+VQDMPVTVAV
Sbjct: 420 GPIAIEAIKDNKAVYLMAVGGAAYLVAQAIKKSKVLAFAELGMEAIYEFEVQDMPVTVAV 479

Query: 494 DSNGTSVHQTGPKEWQARI 512
           D+NG SVH TGP  WQ +I
Sbjct: 480 DTNGESVHITGPAIWQKKI 498


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: 948
Number of extensions: 33
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: 507
Length adjustment: 35
Effective length of query: 485
Effective length of database: 472
Effective search space:   228920
Effective search space used:   228920
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.

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

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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