Alignments for a candidate for fumD in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Shewanella loihica PV-4

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 5209433 Shew_1904 tartrate/fumarate subfamily Fe-S type hydro-lyase alpha subunit (RefSeq)

Query= BRENDA::Q141Z6
         (520 letters)



>FitnessBrowser__PV4:5209433
          Length = 507

 Score =  717 bits (1850), Expect = 0.0
 Identities = 347/507 (68%), Positives = 413/507 (81%), Gaps = 3/507 (0%)

Query: 8   VSTELAMTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTN 67
           +S  +   +IKQ DLI+S+AD+LQYISYYHP D++ A+  AYE E+S AAKDAIAQIL N
Sbjct: 1   MSVTIEQPIIKQADLIESVADALQYISYYHPKDFVDAMAEAYEREESAAAKDAIAQILIN 60

Query: 68  SRMCAEGKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASI 127
           SRM AEGKRP+CQDTGIVT FVK+GM V+WD   M V  M++EGVRR Y NPDN LRASI
Sbjct: 61  SRMSAEGKRPLCQDTGIVTCFVKIGMGVKWDKTDMTVQQMVDEGVRRAYTNPDNPLRASI 120

Query: 128 VSPPEGGRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWIL 187
           V+ P GGRKNTKDNTP+V+H E+VPGN V+V +AAKGGGSENKSK  MLNPSD I +W+ 
Sbjct: 121 VADPAGGRKNTKDNTPSVVHVEMVPGNHVEVAIAAKGGGSENKSKMVMLNPSDDIAEWVE 180

Query: 188 KTVPTMGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVEL 247
           KT+PTMGAGWCPPGMLGIGIGGTAEKA VMAKE+LMDP+DI ++ A+G +   E+LR+++
Sbjct: 181 KTLPTMGAGWCPPGMLGIGIGGTAEKAAVMAKEALMDPVDIHELQAKGAETAEEKLRLDI 240

Query: 248 HEKVNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAAR 307
            E+ N LGIGAQGLGGL TVLD+KI +APTHAASKPV +IPNCAATRH HF LDGSG A 
Sbjct: 241 FERANKLGIGAQGLGGLTTVLDIKIKSAPTHAASKPVVMIPNCAATRHVHFHLDGSGPAE 300

Query: 308 LEAPSLDAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRI 367
           LE P L+ WP++  +   E  +RVDLNT+T  ++  W  G  LLL+GKMLTGRDAAHKRI
Sbjct: 301 LETPKLEDWPEITREAG-EGVRRVDLNTVTQADIEQWKSGDVLLLNGKMLTGRDAAHKRI 359

Query: 368 ADMLAKGEKLP--VDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLI 425
             ++  GE LP  VDFT + IYYVGPVDPV DE VGPAGPTTATRMDKFT++ML +TGL+
Sbjct: 360 QTLIESGEGLPEGVDFTGKFIYYVGPVDPVGDEVVGPAGPTTATRMDKFTDLMLDKTGLM 419

Query: 426 SMIGKAERGPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQ 485
            MIGKAERGP  +E+I+KHKA YLMAVGGAAYLVSKAI+ ++V+AFEDLGMEAIYEFDV 
Sbjct: 420 GMIGKAERGPATVESIKKHKAVYLMAVGGAAYLVSKAIKKSRVVAFEDLGMEAIYEFDVT 479

Query: 486 DMPVTVAVDSNGTSVHQTGPKEWQARI 512
           DMPVTVAVDS G + H+TGP  W+ ++
Sbjct: 480 DMPVTVAVDSEGVNAHETGPATWRVKL 506


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: 886
Number of extensions: 33
Number of successful extensions: 3
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