Alignments for a candidate for actP in Sulfurimonas denitrificans DSM 1251

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Sulfurimonas denitrificans DSM 1251

Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate WP_011373083.1 SUDEN_RS07600 cation acetate symporter

Query= uniprot:A0A1N7U9G2
         (552 letters)



>NCBI__GCF_000012965.1:WP_011373083.1
          Length = 554

 Score =  780 bits (2015), Expect = 0.0
 Identities = 398/543 (73%), Positives = 463/543 (85%), Gaps = 9/543 (1%)

Query: 17  AVWAADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNKSAADYYAAGGKITGFQ 76
           AV+A+DA+TG+V KQ LNVSAIVMF++FV  TL ITYWA+KR KSA D+Y AGG ITGFQ
Sbjct: 14  AVFASDAITGQVQKQDLNVSAIVMFLIFVAGTLGITYWAAKRTKSAKDFYTAGGGITGFQ 73

Query: 77  NGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFA 136
           NG+AIAGDYMSAASFLGIS LVY  GYDGLIYSIGFLVGWPIILF+IAE LRNLGKYTFA
Sbjct: 74  NGMAIAGDYMSAASFLGISGLVYMKGYDGLIYSIGFLVGWPIILFMIAEPLRNLGKYTFA 133

Query: 137 DVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVGILMVL 196
           DVASYRL QT IR+L+A GS+  V  YLIAQMVG+GKLIQLLFGL Y +AVILVGILM+L
Sbjct: 134 DVASYRLKQTPIRTLAASGSIATVVLYLIAQMVGSGKLIQLLFGLSYEMAVILVGILMIL 193

Query: 197 YVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALFSEAIKVHPKGEAIMSP 256
           YV+FGGMLATTWVQIIKA LLLSGASFMA+ VM H +F F ALFS A ++  KG  IMSP
Sbjct: 194 YVVFGGMLATTWVQIIKAFLLLSGASFMAIAVMAHYDFSFGALFSHATEL--KGIEIMSP 251

Query: 257 GGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFI 316
           GGLV DPISA SL +ALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFI
Sbjct: 252 GGLVSDPISAISLAVALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFI 311

Query: 317 IGFGAILLVSTNPAF----KDAAGA---LMGGNNMAAVHLANAVGGSIFLGFISAVAFAT 369
           IGFGAI++V  NP +    KDAA     ++GG+NMAA+HL++AVGG  FLGFISAVAFAT
Sbjct: 312 IGFGAIVMVFKNPQYLDVVKDAASGGSPILGGSNMAAIHLSHAVGGDFFLGFISAVAFAT 371

Query: 370 ILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLAIGLGILFESQ 429
           ILAVV+GLTLAGASA+SHDLYASV +KG+ +   E+RVSKI T+ALGV+AI +GI FE+Q
Sbjct: 372 ILAVVSGLTLAGASAISHDLYASVFRKGRVDSMTEMRVSKIATVALGVVAIFMGIAFENQ 431

Query: 430 NIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMVLGPTIWVSI 489
           NIAF+VGLAF+IAAS NFP+L+LSMYW+ LTTRGA+IGG LGL SAV L++L P +WV I
Sbjct: 432 NIAFVVGLAFAIAASANFPILVLSMYWRKLTTRGAVIGGTLGLASAVILVILSPVVWVDI 491

Query: 490 LHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRSQTGLGSSGA 549
           +H+ +AIFPY+YPALFS+ +AF+  WFFS+TDKS  A+ E+  +  QF+R+QTG+G+ GA
Sbjct: 492 MHNAQAIFPYKYPALFSVSVAFIATWFFSVTDKSQDAKDEQERFDAQFIRAQTGIGAEGA 551

Query: 550 VSH 552
            SH
Sbjct: 552 SSH 554


Lambda     K      H
   0.327    0.140    0.415 

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: 1022
Number of extensions: 44
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: 552
Length of database: 554
Length adjustment: 36
Effective length of query: 516
Effective length of database: 518
Effective search space:   267288
Effective search space used:   267288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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