Alignments for a candidate for cstA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for cstA in Pseudomonas simiae WCS417

Align Carbon starvation protein A (characterized, see rationale)
to candidate GFF4750 PS417_24295 carbon starvation protein A

Query= uniprot:A0A0N9VZ52
         (685 letters)



>FitnessBrowser__WCS417:GFF4750
          Length = 688

 Score = 1276 bits (3302), Expect = 0.0
 Identities = 634/682 (92%), Positives = 666/682 (97%)

Query: 4   LAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQL 63
           L +HL W  +A++GA AL VVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIAN VMQL
Sbjct: 7   LLRHLPWLVLAIVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANNVMQL 66

Query: 64  DPGRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG 123
           DP RATPAV+NNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG
Sbjct: 67  DPRRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG 126

Query: 124 VVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVV 183
           VVLAGAVQDFM+LF+STRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALIVV
Sbjct: 127 VVLAGAVQDFMILFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVV 186

Query: 184 KALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADP 243
           KALA+SPWG+FTVMATIPIAMFMG+YMRYIRPGRIGEIS++GVLLLLGSIWLGGQIAADP
Sbjct: 187 KALAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISIIGVLLLLGSIWLGGQIAADP 246

Query: 244 VWAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMP 303
           VWAKAF+FTGIQITWMLIGYGFVAAV+PVWLILAPRDYLSTFLKIGTI+ALAIGIL+TMP
Sbjct: 247 VWAKAFTFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIIALAIGILVTMP 306

Query: 304 ELKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYI 363
           +LKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALI+SGTTPKLLA+E HARYI
Sbjct: 307 DLKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLANESHARYI 366

Query: 364 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEAL 423
           GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVG DVV VAQTVSSWGF ITPEAL
Sbjct: 367 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGTDVVTVAQTVSSWGFAITPEAL 426

Query: 424 QAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD 483
            AVA DIGETT+LARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD
Sbjct: 427 SAVAHDIGETTILARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD 486

Query: 484 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW 543
           AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW
Sbjct: 487 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW 546

Query: 544 PLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAI 603
           PLFGISNQMLAGIALML+TVVLIKMKRQRYIWVT+LPA WLLICTTTAGFIKLFDANPAI
Sbjct: 547 PLFGISNQMLAGIALMLATVVLIKMKRQRYIWVTMLPAVWLLICTTTAGFIKLFDANPAI 606

Query: 604 GFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVG 663
           GFLSLAKKYSDALANGQILAPAK+I QMQHVI+NAYTNATLTALFLFVVFSILFYA+KVG
Sbjct: 607 GFLSLAKKYSDALANGQILAPAKNIDQMQHVIWNAYTNATLTALFLFVVFSILFYALKVG 666

Query: 664 ISAWGSKERTDKESPFQAIPEA 685
           ++AWG+KERTDKE+PFQA+P+A
Sbjct: 667 VAAWGNKERTDKEAPFQAVPDA 688


Lambda     K      H
   0.328    0.141    0.433 

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: 1659
Number of extensions: 46
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: 685
Length of database: 688
Length adjustment: 39
Effective length of query: 646
Effective length of database: 649
Effective search space:   419254
Effective search space used:   419254
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: 54 (25.4 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