GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1444
          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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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:

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:

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:

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:

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