GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_4641
          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:

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