GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Rhodobacter maris JA276

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_097070748.1 CRO22_RS13790 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_900217815.1:WP_097070748.1
          Length = 358

 Score =  125 bits (315), Expect = 2e-33
 Identities = 97/302 (32%), Positives = 154/302 (50%), Gaps = 21/302 (6%)

Query: 140 IQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYS-YALLSSYFGLSFWVLLPLSGIF 198
           +  LIY + A GLNI+VG AG + LG   F AVGAY+ Y L++++  + F+  + L+G  
Sbjct: 54  VPFLIYAIAAIGLNILVGFAGQVSLGTGGFMAVGAYAVYKLMTAFPEVPFFFHVILAGGV 113

Query: 199 AALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTD--VTKGTFGISSIPKATLFG 256
            A  GV+ G P LR++G YLA+ TLA  +   + L N           G  + P  T+ G
Sbjct: 114 TACVGVLFGLPSLRIKGFYLAVATLA-AQFFLVWLFNKVPWFYNYSASGQITAPDRTMLG 172

Query: 257 IPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALRED 316
           I                 +SA  K +LF L++    L A V   L R  +GR W A+R+ 
Sbjct: 173 IYITGAQ-----------TSAVAK-YLFCLVILT--LVALVARNLTRGTVGRKWMAIRDM 218

Query: 317 EIACRSLGINTVTTKLTAFATGAMFAGFAGS-FFAARQGFVS-PESFVFLESAVILAIVV 374
           +IA   +G+N +T K+TAFA  + F G AG+  F+   G     E+F   +S ++L +V+
Sbjct: 219 DIAAEIIGVNPLTAKVTAFAVSSFFIGIAGALLFSVYLGAAEVGEAFGINKSFLVLFMVI 278

Query: 375 LGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKP 434
           +GG+GS+ G    A  +V     L+ +      +  D    L  ++I G  +++ ++ +P
Sbjct: 279 IGGLGSIFGSFAGAAFLVLLPVFLKNVLVGAFGWPTDVAAHL-ELMIVGALIILFLIVEP 337

Query: 435 RG 436
            G
Sbjct: 338 HG 339


Lambda     K      H
   0.330    0.145    0.432 

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: 478
Number of extensions: 27
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: 463
Length of database: 358
Length adjustment: 31
Effective length of query: 432
Effective length of database: 327
Effective search space:   141264
Effective search space used:   141264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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 24 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