GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas simiae WCS417

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF1300 PS417_06605 leucine/isoleucine/valine transporter permease subunit

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__WCS417:GFF1300
          Length = 417

 Score =  599 bits (1544), Expect = e-176
 Identities = 306/417 (73%), Positives = 351/417 (84%), Gaps = 2/417 (0%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60
           MS+ LK A FSALLV  V++P+LGLKL  VGI LEV G    TL  IA  ++ MF+  LF
Sbjct: 1   MSRYLKSAFFSALLVWAVAFPVLGLKLSIVGINLEVHGTGPVTLTIIALCSVLMFLRVLF 60

Query: 61  RDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLI 120
             ++        G  V+   +  FL+LP TQR+ ++AL++ A +WPFF SRGAVDIATLI
Sbjct: 61  TQQVGALFKSNRGPLVSPK-VSQFLTLPRTQRYIIIALIIAALIWPFFGSRGAVDIATLI 119

Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180
           LIYV+LG+GLNIVVGLAGLLDLGYVGFYAVGAYTYALL+ Y G+ FW  LP+AGM AA F
Sbjct: 120 LIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYALLSHYLGWSFWICLPLAGMAAATF 179

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240
           GFLLGFPVLRLRGDYLAIVTLGFGEIIR+ LRN+T+ITGGPNGI SIPKPT FGL+F+R 
Sbjct: 180 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISSIPKPTFFGLSFDRT 239

Query: 241 APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300
           A EGMQTFHE+FGI YN   KV+ LY+VALLL L ALFVINRL+RMPIGRAWEALREDE+
Sbjct: 240 AAEGMQTFHEYFGIDYNPVSKVVFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 299

Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360
           ACRALGLNPTI+KLSAFT+GA+FAGFAGSFFAARQGLVTPESFTFIESA+ILAIVVLGGM
Sbjct: 300 ACRALGLNPTIIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 359

Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           GSQLGVILAA+VM+LL E MR F+EYRML+FG  M++MMIWRPQGLLPMQRPH+EL+
Sbjct: 360 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGAMMVLMMIWRPQGLLPMQRPHMELR 416


Lambda     K      H
   0.330    0.146    0.439 

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: 642
Number of extensions: 28
Number of successful extensions: 4
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: 417
Length of database: 417
Length adjustment: 31
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 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