GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Sinorhizobium meliloti 1021

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 SMc01950 SMc01950 high-affinity branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Smeli:SMc01950
          Length = 461

 Score =  342 bits (876), Expect = 2e-98
 Identities = 185/327 (56%), Positives = 226/327 (69%), Gaps = 18/327 (5%)

Query: 99  VVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALL 158
           V+VA V    + +   +    ILIYVML  GLNIVVGLAGLLDLGYV FYAVGAY+YALL
Sbjct: 119 VIVALVGVQGSLKWVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALL 178

Query: 159 AEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEIT 218
           + Y G  FW  LPIAG++AA +G +LGFPVLRLRGDYLAIVTL FGEIIR++L N TE+T
Sbjct: 179 SSYFGLSFWVLLPIAGLLAACWGVVLGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTEVT 238

Query: 219 GGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALF 278
            G  G+  I K TLFG+ F+         F    G+  ++ Y  I L+ + L L LL  F
Sbjct: 239 KGTFGVSGIAKATLFGIKFDAT----KDGFAAMMGLPMSSAYYKIFLFYLILGLALLTAF 294

Query: 279 VINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLV 338
           V  RL RMPIGRAWEALREDE+ACR+LG+N    KL+AF  GA F GFAGSFFA RQG V
Sbjct: 295 VTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFGGFAGSFFAVRQGFV 354

Query: 339 TPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMV----LLQEMRGFNE---------- 384
           +PESF F+ESA+ILAIVVLGGMGS  G+ +AAVVM+    +L+E+               
Sbjct: 355 SPESFVFLESAVILAIVVLGGMGSLTGIAIAAVVMIGGTEILRELTFLKMIFGPTFTPEL 414

Query: 385 YRMLIFGLTMIVMMIWRPQGLLPMQRP 411
           YRMLIFGL M+V+M+W+P+G +  + P
Sbjct: 415 YRMLIFGLAMVVVMVWKPRGFVGSREP 441


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: 601
Number of extensions: 39
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: 417
Length of database: 461
Length adjustment: 32
Effective length of query: 385
Effective length of database: 429
Effective search space:   165165
Effective search space used:   165165
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: 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