Alignments for a candidate for cstA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for cstA in Pseudomonas fluorescens FW300-N2C3

Align Carbon starvation protein A (characterized, see rationale)
to candidate AO356_25680 AO356_25680 carbon starvation protein A

Query= uniprot:A0A0N9VZ52
         (685 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25680
          Length = 686

 Score = 1277 bits (3304), Expect = 0.0
 Identities = 638/684 (93%), Positives = 668/684 (97%)

Query: 2   TRLAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVM 61
           TRL KHLAWFAVAVLGA ALSVVALRRGE INALWIVVAAVAIYLVAYRYYSLFIAN VM
Sbjct: 3   TRLVKHLAWFAVAVLGACALSVVALRRGEPINALWIVVAAVAIYLVAYRYYSLFIANNVM 62

Query: 62  QLDPGRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLI 121
           QLD  RATPAV+NNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLI
Sbjct: 63  QLDARRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLI 122

Query: 122 AGVVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALI 181
           AGVVLAGAVQDFMVLF+STRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALI
Sbjct: 123 AGVVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALI 182

Query: 182 VVKALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAA 241
           VVKALA+SPWG+FTVMATIPIAMFMG+YMRYIRPGRIGEIS++GVLLLLGSIWLGGQIAA
Sbjct: 183 VVKALAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISIIGVLLLLGSIWLGGQIAA 242

Query: 242 DPVWAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILIT 301
           DPVWAKAF+FTGIQITWMLIGYGFVAAV+PVWLILAPRDYLSTFLKIGTI+ALAIGIL+T
Sbjct: 243 DPVWAKAFTFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILVT 302

Query: 302 MPELKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHAR 361
           MPELKMPALTQF DGTGPVWKGGLFPFLFITIACGAVSGFHALI+SGTTPKLL +E +AR
Sbjct: 303 MPELKMPALTQFTDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNAR 362

Query: 362 YIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPE 421
           YIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVV VAQTVSSWGF ITPE
Sbjct: 363 YIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVAVAQTVSSWGFAITPE 422

Query: 422 ALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTA 481
           ALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTA
Sbjct: 423 ALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTA 482

Query: 482 VDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINT 541
           VDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVA+WGYLLYQGVIDPLGGINT
Sbjct: 483 VDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVALWGYLLYQGVIDPLGGINT 542

Query: 542 LWPLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANP 601
           LWPLFGISNQMLAGIALML+TVVLIKMKRQRY+WVTLLPA+WLLICTTTAG IKLFDANP
Sbjct: 543 LWPLFGISNQMLAGIALMLATVVLIKMKRQRYVWVTLLPASWLLICTTTAGLIKLFDANP 602

Query: 602 AIGFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIK 661
           AIGFL+LA+KY+DALA GQILAPAK I QMQHV++NAYTNATLT LFLFVVFSILFYA+K
Sbjct: 603 AIGFLALARKYNDALAAGQILAPAKSIEQMQHVVFNAYTNATLTVLFLFVVFSILFYALK 662

Query: 662 VGISAWGSKERTDKESPFQAIPEA 685
           VGI+AWG+KERTDKE+PFQA+P+A
Sbjct: 663 VGIAAWGTKERTDKEAPFQALPDA 686


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: 1630
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: 686
Length adjustment: 39
Effective length of query: 646
Effective length of database: 647
Effective search space:   417962
Effective search space used:   417962
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