GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM 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)



>lcl|FitnessBrowser__WCS417:GFF1300 PS417_06605
           leucine/isoleucine/valine transporter permease subunit
          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.

Links

Downloads

Related tools

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 preprint 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