GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc01950
          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 (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