Aligments for a candidate for cstA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for cstA in Pseudomonas fluorescens GW456-L13

Align Carbon starvation protein A (characterized, see rationale)
to candidate PfGW456L13_1444 Carbon starvation protein A

Query= uniprot:A0A0N9VZ52
         (685 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1444 Carbon
           starvation protein A
          Length = 688

 Score = 1272 bits (3291), Expect = 0.0
 Identities = 634/680 (93%), Positives = 662/680 (97%)

Query: 6   KHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQLDP 65
           +HL W  +A++GA AL VVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIAN VMQLD 
Sbjct: 9   RHLPWLVLAIVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANNVMQLDA 68

Query: 66  GRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV 125
            RATPAV+NNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV
Sbjct: 69  RRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV 128

Query: 126 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVVKA 185
           LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALIVVKA
Sbjct: 129 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVVKA 188

Query: 186 LADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADPVW 245
           LA+SPWG+FTVMATIPIAMFMG+YMRYIRPGRIGEISV+GVLLLLGSIWLGGQIAADPVW
Sbjct: 189 LAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVLLLLGSIWLGGQIAADPVW 248

Query: 246 AKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMPEL 305
           AKAFSFTGIQITWMLIGYGFVAAV+PVWLILAPRDYLSTFLKIGTI+ALAIGIL+TMPEL
Sbjct: 249 AKAFSFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILVTMPEL 308

Query: 306 KMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYIGY 365
           KMPALTQF+DGTGPVWKGGLFPFLFITIACGAVSGFHALI+SGTTPKLL +E +ARYIGY
Sbjct: 309 KMPALTQFVDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYIGY 368

Query: 366 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEALQA 425
           GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAA+VGGDVV VA  VS+WGF ITPEALQA
Sbjct: 369 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVGGDVVAVATAVSNWGFAITPEALQA 428

Query: 426 VAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDAG 485
           VA DIGETT+LARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDAG
Sbjct: 429 VAHDIGETTILARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDAG 488

Query: 486 TRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLWPL 545
           TRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWG+LLYQGVIDPLGGINTLWPL
Sbjct: 489 TRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGWLLYQGVIDPLGGINTLWPL 548

Query: 546 FGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAIGF 605
           FGISNQMLAGIALML TVVLIKMKRQRY+WVT+LPA WLLICTTTAGFIKLFDANPAIGF
Sbjct: 549 FGISNQMLAGIALMLGTVVLIKMKRQRYVWVTMLPAVWLLICTTTAGFIKLFDANPAIGF 608

Query: 606 LSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVGIS 665
           LSLAKKYSDALANGQILAPAKDITQMQHVI+NAYTNATLTALFLFVVFSILFYA+KVGI+
Sbjct: 609 LSLAKKYSDALANGQILAPAKDITQMQHVIFNAYTNATLTALFLFVVFSILFYALKVGIA 668

Query: 666 AWGSKERTDKESPFQAIPEA 685
           AWG KERTDKESPFQA+P+A
Sbjct: 669 AWGKKERTDKESPFQALPDA 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: 1666
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, or view the source code.

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