Alignments for a candidate for praB in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for praB in Desulfobacter vibrioformis DSM 8776

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  347 bits (891), Expect = e-100
 Identities = 196/486 (40%), Positives = 291/486 (59%), Gaps = 7/486 (1%)

Query: 1   MQQTKVKPIDCLH-FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKK 59
           M + K   + C H FI  ++V +  GKT D  NPAT + LGTV   GA E   A+ AA +
Sbjct: 1   MLKIKNTALFCRHCFIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANE 60

Query: 60  ALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFH 119
           +L+  W+  TA ER A+LRK  DL++E +E+L+V+ + + GKP   S   +I  AA  F 
Sbjct: 61  SLDA-WRSKTAGERSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRG-EIAYAAAFFE 118

Query: 120 FFSDYIRTITNEATQMDDVALNYA-IRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTV 178
           +F++  + +  +       +     I++PVGV+  I PWN P  ++T K   ALAAG T+
Sbjct: 119 WFAEEAKRVYGDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTM 178

Query: 179 VMKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETT 238
           V+KPA  TP +A  +A++ + AGVP GV N+V G   ++ G  LT +P V  ++FTG T 
Sbjct: 179 VLKPATATPFSALAIAKLGQQAGVPKGVFNVVTG-SSSAIGGELTANPIVRKLTFTGSTQ 237

Query: 239 TGKIIMASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIY 298
            GK +M   A T+KRLS ELGG  P ++F D+++D  +E  M   + N G+ C+C +R+Y
Sbjct: 238 VGKKLMRDCAGTMKRLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMY 297

Query: 299 VERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILT 358
           V+   Y+ F  K  A  +EL VG+ FD   + G LI     E V  +IK AV++GG +L 
Sbjct: 298 VQAGVYDEFCRKLTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLA 357

Query: 359 GGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGL 418
           GG R   L + +F  PTII  +T D RV +EE FGP+  V  FDTEEEV+ + NDT +GL
Sbjct: 358 GGTR-HALGRTFF-APTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGL 415

Query: 419 SASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478
           +A  +T D+ R+ R+  ++E G+V +N+  + +   PFGG+K+SG GREG  +  + Y E
Sbjct: 416 AAYFYTRDMARSWRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLE 475

Query: 479 LTNICI 484
           +  +C+
Sbjct: 476 IKYMCM 481


Lambda     K      H
   0.318    0.136    0.404 

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: 631
Number of extensions: 34
Number of successful extensions: 5
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: 486
Length of database: 484
Length adjustment: 34
Effective length of query: 452
Effective length of database: 450
Effective search space:   203400
Effective search space used:   203400
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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