GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cstA in Pseudomonas putida KT2440

Align Carbon starvation protein A (characterized, see rationale)
to candidate PP_4641 PP_4641 putative transporter

Query= uniprot:A0A0N9VZ52
         (685 letters)



>lcl|FitnessBrowser__Putida:PP_4641 PP_4641 putative transporter
          Length = 688

 Score = 1214 bits (3140), Expect = 0.0
 Identities = 606/682 (88%), Positives = 642/682 (94%)

Query: 4   LAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQL 63
           L +H+ W A+AV+GA AL VVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIA KVMQL
Sbjct: 7   LLRHIPWLALAVIGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIATKVMQL 66

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

Query: 124 VVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVV 183
           VVLAGAVQDFMVLF+STRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALIVV
Sbjct: 127 VVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVV 186

Query: 184 KALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADP 243
           KALA+SPWGMFTVMATIPIAMFMG+YMRYIRPGRIGEISVVGV+LLL SIWLGG IAADP
Sbjct: 187 KALAESPWGMFTVMATIPIAMFMGIYMRYIRPGRIGEISVVGVVLLLASIWLGGVIAADP 246

Query: 244 VWAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMP 303
           VW  AF+FTG+QITWML+GYGFVAAV+PVWL+LAPRDYLSTFLKIGTI+ LAIGILI  P
Sbjct: 247 VWGPAFTFTGVQITWMLVGYGFVAAVLPVWLVLAPRDYLSTFLKIGTILGLAIGILIIAP 306

Query: 304 ELKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYI 363
           ELKMPALTQF DGTGPVWKG LFPFLFITIACGAVSGFHALI+SGTTPKLL +E +ARYI
Sbjct: 307 ELKMPALTQFTDGTGPVWKGTLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYI 366

Query: 364 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEAL 423
           GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAA+VG DV  VAQTVSSWGF+ITPE L
Sbjct: 367 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVGTDVASVAQTVSSWGFLITPEQL 426

Query: 424 QAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD 483
           +AVA+DIGE T+LARAGGAPTLAVGIAQILH VLPGENTMAFWYHFAILFEALFILTAVD
Sbjct: 427 EAVARDIGEHTILARAGGAPTLAVGIAQILHQVLPGENTMAFWYHFAILFEALFILTAVD 486

Query: 484 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW 543
           AGTRAGRFMLQDLLGSFVPALKRTESW ANL+ATAGCVA+WGYLLYQGVIDPLGGINTLW
Sbjct: 487 AGTRAGRFMLQDLLGSFVPALKRTESWGANLLATAGCVALWGYLLYQGVIDPLGGINTLW 546

Query: 544 PLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAI 603
           PLFGISNQMLAGIALML TVVLIKMKRQRYIWVTLLPA WLLICTT AG IKLFD NPA+
Sbjct: 547 PLFGISNQMLAGIALMLGTVVLIKMKRQRYIWVTLLPAVWLLICTTAAGLIKLFDPNPAV 606

Query: 604 GFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVG 663
           GFL+LAKKYS AL  GQ+LAPAKDI QMQHVI+NAYTNA LT LFL VVFSILF+AIKVG
Sbjct: 607 GFLALAKKYSTALDAGQVLAPAKDIGQMQHVIFNAYTNAGLTILFLLVVFSILFFAIKVG 666

Query: 664 ISAWGSKERTDKESPFQAIPEA 685
            +A G KER+DKE+PFQA+P+A
Sbjct: 667 YAALGRKERSDKETPFQALPDA 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: 1632
Number of extensions: 51
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 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