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

GapMind for catabolism of small carbon sources

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

Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 5210577 Shew_3005 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein (RefSeq)

Query= uniprot:Q8EGS5
         (464 letters)



>FitnessBrowser__PV4:5210577
          Length = 462

 Score =  838 bits (2165), Expect = 0.0
 Identities = 402/454 (88%), Positives = 428/454 (94%)

Query: 9   AMGSQVHAYKADIFCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLGSEIKLHTL 68
           A+ S VHA KADIFC+DE RVDWHSKALW+LREKRDRAA SLPEWEQLRQLGSE+KLHTL
Sbjct: 7   ALNSGVHAKKADIFCQDEARVDWHSKALWVLREKRDRAAASLPEWEQLRQLGSEMKLHTL 66

Query: 69  TNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSMLTEECHLN 128
           T+L +YLETFE+NC ANGI VHWAKDGAEHN+IVH ILA H+VKKLVKSKSMLTEECHLN
Sbjct: 67  THLGEYLETFEKNCQANGIVVHWAKDGAEHNQIVHNILAKHQVKKLVKSKSMLTEECHLN 126

Query: 129 PYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESDPL 188
           PYLE +GIEVIDTDLGERIIQLAK PPSHIVVPAIH+KKEEVGDLFHDKLGT+AG SDPL
Sbjct: 127 PYLESKGIEVIDTDLGERIIQLAKQPPSHIVVPAIHLKKEEVGDLFHDKLGTEAGASDPL 186

Query: 189 YLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGID 248
           YLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGID
Sbjct: 187 YLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGID 246

Query: 249 KVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTEMMKDKILA 308
           K+VPD+DSAA+LLRTLARNATGQP+TTYS+FYRGPQ  GEMHVIIVDNGRT+M++DKILA
Sbjct: 247 KIVPDLDSAAILLRTLARNATGQPITTYSSFYRGPQDGGEMHVIIVDNGRTDMLQDKILA 306

Query: 309 ESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHDNTNSIAWACTLCGSCTY 368
           ESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGA  D+T+SI WACTLCGSC+Y
Sbjct: 307 ESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGAQADDTHSIPWACTLCGSCSY 366

Query: 369 VCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMASTTLLNCSMGAARTALRIL 428
           VCPTKVPLDKIIHHHRRLKA+AGKLPYGK  YMPLVG FMAS T+LNCSM  ARTALRIL
Sbjct: 367 VCPTKVPLDKIIHHHRRLKAKAGKLPYGKRNYMPLVGNFMASETMLNCSMSVARTALRIL 426

Query: 429 PGSLLKPFSGAWGKYRELPVAPNSSFEAWFKKHR 462
           PGSLLKPFSGAWGKYRELPVAP SSFEAWF K+R
Sbjct: 427 PGSLLKPFSGAWGKYRELPVAPKSSFEAWFNKNR 460


Lambda     K      H
   0.320    0.134    0.413 

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: 789
Number of extensions: 11
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: 464
Length of database: 462
Length adjustment: 33
Effective length of query: 431
Effective length of database: 429
Effective search space:   184899
Effective search space used:   184899
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 (21.8 bits)
S2: 51 (24.3 bits)

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

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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, or view the source code.

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