Alignments for a candidate for actP in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas stutzeri RCH2

Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate GFF2882 Psest_2938 transporter, SSS family

Query= uniprot:A0A1N7U9G2
         (552 letters)



>FitnessBrowser__psRCH2:GFF2882
          Length = 551

 Score =  852 bits (2200), Expect = 0.0
 Identities = 433/552 (78%), Positives = 486/552 (88%), Gaps = 1/552 (0%)

Query: 1   MIRRLLAILGASIFAPAVWAADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNK 60
           MI R L        +PA+  ADA+TGEV KQ  N +AI+MFVVF+  T+ IT WA+KRN 
Sbjct: 1   MILRFLMTALLLAVSPAL-LADAITGEVEKQATNYTAIIMFVVFIAFTMGITKWAAKRNT 59

Query: 61  SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIIL 120
           S ADYY AGG ITGFQNGLAIAGD+MSAASFLGISALVYTSGYDGLIYSIGFLVGWPIIL
Sbjct: 60  STADYYTAGGSITGFQNGLAIAGDFMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIIL 119

Query: 121 FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG 180
           FL+AERLRNLGK+TF+DVASYRLGQTQIR LSA GSL+VVAFYLIAQMVGAGKLIQLLFG
Sbjct: 120 FLMAERLRNLGKFTFSDVASYRLGQTQIRLLSAFGSLIVVAFYLIAQMVGAGKLIQLLFG 179

Query: 181 LDYHVAVILVGILMVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF 240
           LDY+VAV+LVG+LMV+YVLFGGMLATTWVQIIKAVLLLSGASFMA+MVMK V FDF +LF
Sbjct: 180 LDYYVAVVLVGVLMVMYVLFGGMLATTWVQIIKAVLLLSGASFMAIMVMKSVGFDFGSLF 239

Query: 241 SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 300
           +EA+K+H KG  IMSPGGLV DPISA SLGLALMFGTAGLPHILMRFFTVSDAKEARKSV
Sbjct: 240 AEAVKIHEKGAQIMSPGGLVSDPISAISLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 299

Query: 301 FYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSIFLG 360
           FYATGFIGYFYILTFIIGFGAILLVSTNP FKD  GA++GG NM A+HLA+AVGG++FLG
Sbjct: 300 FYATGFIGYFYILTFIIGFGAILLVSTNPEFKDVTGAIVGGTNMVAIHLASAVGGNLFLG 359

Query: 361 FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLAI 420
           FISAVAFATILAVVAGLTLAGASAVSHDLYA VIK+GKA ++DE+RV+K+TT+ LGV+AI
Sbjct: 360 FISAVAFATILAVVAGLTLAGASAVSHDLYACVIKQGKAREEDEMRVTKLTTLTLGVVAI 419

Query: 421 GLGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMV 480
            LGI+FE QNIAFMVGLAFSIAASCNFPVL LSMYWK L+TRGA+ GG LGL +A+ L +
Sbjct: 420 LLGIIFEKQNIAFMVGLAFSIAASCNFPVLFLSMYWKGLSTRGALFGGSLGLFTALLLTI 479

Query: 481 LGPTIWVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRS 540
           + PT+WV +    +AIFPY+YPALFSM  AF GIWFFS+TDKS  A +ER  +F QFVRS
Sbjct: 480 ISPTVWVDVFGFAEAIFPYKYPALFSMAAAFAGIWFFSVTDKSKRAGEERERFFAQFVRS 539

Query: 541 QTGLGSSGAVSH 552
           QTGLG++GAV+H
Sbjct: 540 QTGLGATGAVAH 551


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: 1105
Number of extensions: 46
Number of successful extensions: 1
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: 551
Length adjustment: 36
Effective length of query: 516
Effective length of database: 515
Effective search space:   265740
Effective search space used:   265740
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 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