GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsS in Pseudomonas simiae WCS417

Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate GFF4503 PS417_23050 trehalose permease IIC protein

Query= BRENDA::P12655
         (664 letters)



>FitnessBrowser__WCS417:GFF4503
          Length = 480

 Score =  362 bits (929), Expect = e-104
 Identities = 193/475 (40%), Positives = 302/475 (63%), Gaps = 14/475 (2%)

Query: 2   DYSKVASEVITAVG-KDNLVAAAHCATRLRLVLKDDSKVDQKALDKNADVKGTFKTDGQY 60
           DYS +A E++  +G  DNL  AAHC TRLRL LKD S V+  AL++   VKG+F T G +
Sbjct: 4   DYSTIAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTGGLF 63

Query: 61  QVIIGPGDVNFVYDEIIKQTGLTEVSTDDLKKIAASGKKFNPIMALIKLLSDIFVPIIPA 120
           QV+IGPG+V  VY  + +QTGL   +  D+KK  A   K N +  L+++ SD+F+PI+PA
Sbjct: 64  QVVIGPGEVEKVYAALREQTGLAAATIADVKKKGAD--KTNAMQRLVRVFSDVFMPILPA 121

Query: 121 LVAGGLLMALNNFLTSEGLF-GTKSLVQQFPIIKGSSDMIQLMSAAPFWFLPILVGISAA 179
           L+  GLLM +NN + ++G+F   K+L++ +P + G   +I LM+   F FLP LVG SAA
Sbjct: 122 LIIAGLLMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSAA 181

Query: 180 KRFGANQFLGASIGMIMVAPGAANIIGLAANAPISKAATIGAYTGFWNIFG-LHVTQASY 238
           KRFG ++ LG  +G+++V P   N    A N   + A   G    +++IFG   + +  Y
Sbjct: 182 KRFGGSEILGIVLGLMLVHPDLLN----AWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGY 237

Query: 239 TYQVIPVLVAVWLLSILEKFFHKRLPSAVDFTFTPLLSVIITGFLTFIVIGPVMKEVSDW 298
             Q++P+L+A +++S++EK    R+P+A+     P+ ++++TG L   +IGPV + +   
Sbjct: 238 QGQILPILMAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGIL 297

Query: 299 LTNGIVWLYDTTGFLGMGVFGALYSPVVMTGLHQSFPAIETQLISAFQNGTGHGDFIFVT 358
           +T G+V L+D    +G  +FG LY+P+V+TG+H  F A++ QLIS     T  G FI+  
Sbjct: 298 ITEGVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLIS-----TQGGTFIWPM 352

Query: 359 ASMANVAQGAATFAIYFLTKDKKMKGLSSSSGVSALLGITEPALFGVNLKYRFPFFCALI 418
             M+N+AQG+A  A+++ T++ + K ++S+S +SA  GITEPA+FGVNL+++FPF+ AL+
Sbjct: 353 IVMSNLAQGSAALAVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALV 412

Query: 419 GSASAAAIAGLLQVVAVSLGSAGFLGFLSIKASSIPFYVVCELISFAIAFAVTYG 473
           GSA  +    L +V A ++G  G  GF+SI   SI  +V+  +I+  + F +T G
Sbjct: 413 GSALGSIFLALNKVQASAIGVGGLPGFISIVPQSIAVFVIGMVIAMVVPFVLTCG 467


Lambda     K      H
   0.320    0.135    0.384 

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: 680
Number of extensions: 30
Number of successful extensions: 5
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: 664
Length of database: 480
Length adjustment: 36
Effective length of query: 628
Effective length of database: 444
Effective search space:   278832
Effective search space used:   278832
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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