GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Sinorhizobium meliloti 1021

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate SMc01950 SMc01950 high-affinity branched-chain amino acid ABC transporter permease

Query= uniprot:A0A159ZYE0
         (418 letters)



>lcl|FitnessBrowser__Smeli:SMc01950 SMc01950 high-affinity
           branched-chain amino acid ABC transporter permease
          Length = 461

 Score =  365 bits (936), Expect = e-105
 Identities = 218/435 (50%), Positives = 277/435 (63%), Gaps = 24/435 (5%)

Query: 3   RHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSP-AILAT-IAVCSLLMFLRVLF 60
           R L+ A+F+ L+   +    +GLK T   I  E+  T    +LAT +A+  +  FL V +
Sbjct: 18  RALREAVFAGLITLGMFVLFVGLK-TDQNIRNELILTQRWGLLATFVAIAMVGRFLMVAY 76

Query: 61  STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAV----DI 116
                A  K++        K   F +   ++  ++L LI   ++    G +G++    + 
Sbjct: 77  VQPRLAQRKAAKAAAPDVVKEETFFSRNWSKIAVILLLIYPPVIVALVGVQGSLKWVDNF 136

Query: 117 ATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMM 176
              ILIYVML  GLNIVVGLAGLLDLGYV FYAVGAYSYALLS YFGLSFW+ LPIAG++
Sbjct: 137 GIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPIAGLL 196

Query: 177 AATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLT 236
           AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N T++T G  G+S I K T FG+ 
Sbjct: 197 AACWGVVLGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTEVTKGTFGVSGIAKATLFGIK 256

Query: 237 FERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALR 296
           F+         F    GL  +S    IFL+ + L LAL   FV  RL RMPIGRAWEALR
Sbjct: 257 FDATK----DGFAAMMGLPMSSAYYKIFLFYLILGLALLTAFVTIRLRRMPIGRAWEALR 312

Query: 297 EDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVV 356
           EDEIACR+LG+N    KL+AF  GA F GFAGSFFA RQG V+PESF F+ESA+ILAIVV
Sbjct: 313 EDEIACRSLGINTVTTKLTAFATGAMFGGFAGSFFAVRQGFVSPESFVFLESAVILAIVV 372

Query: 357 LGGMGSQLGVILAAIVMILLPEMMREFS-------------EYRMLMFGALMVLMMIWRP 403
           LGGMGS  G+ +AA+VMI   E++RE +              YRML+FG  MV++M+W+P
Sbjct: 373 LGGMGSLTGIAIAAVVMIGGTEILRELTFLKMIFGPTFTPELYRMLIFGLAMVVVMVWKP 432

Query: 404 QGLLPMQRPHMELRK 418
           +G +  + P   LR+
Sbjct: 433 RGFVGSREPTAFLRE 447


Lambda     K      H
   0.331    0.145    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: 636
Number of extensions: 34
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: 418
Length of database: 461
Length adjustment: 32
Effective length of query: 386
Effective length of database: 429
Effective search space:   165594
Effective search space used:   165594
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 (21.9 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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