GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Cupriavidus basilensis 4G11

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 RR42_RS34790 RR42_RS34790 ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Cup4G11:RR42_RS34790
          Length = 348

 Score =  157 bits (397), Expect = 5e-43
 Identities = 97/318 (30%), Positives = 171/318 (53%), Gaps = 29/318 (9%)

Query: 93  WAVLALVVVAFVWPFFASRGA-VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVG 151
           WA+L  + +AF  P        + + TL  IY +  +GLN++ G  G L+L + GF A+G
Sbjct: 11  WALLLALAIAF--PLVTPNSYYLTVMTLAFIYAIATLGLNLITGYTGQLNLAHGGFMAIG 68

Query: 152 AYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILL 211
           AYT  +L       FW A  ++G++  + G+ +G   LRL+G Y +I TL  G II +L+
Sbjct: 69  AYTLGILTVDHQVPFWAAFVLSGVVCMMVGYFVGVVSLRLKGHYFSIFTLCIGYIIYLLI 128

Query: 212 RNMTEITGGPNGIGSIPKPTLFG-LTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVAL 270
                +T G  G+  IP P   G L F+                     Y ++L ++VA 
Sbjct: 129 EKWESLTHGTVGLIGIPVPASVGPLAFDN----------------VQAQYYLVLFFLVA- 171

Query: 271 LLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSF 330
                  F+++R++   +GR++ A+R  +    ALG+N    K+ +F +   +AGFAG+ 
Sbjct: 172 -----GTFLMHRIVTSLLGRSFMAVRNSDALAEALGINLMRTKVLSFVLSVGYAGFAGAL 226

Query: 331 FAARQGLVTPE-SFTFIESAMILAIVVLGGMGSQLGVILAAVVMV-LLQEMRGFNEYRML 388
           +A +   + P+ + T +   M++A++V GG G+ LG +L AV++  + Q ++   +YRML
Sbjct: 227 YAGQVRFLGPDIARTDLTFEMVMAMLV-GGTGTLLGPLLGAVLVPWVTQTLQFLQDYRML 285

Query: 389 IFGLTMIVMMIWRPQGLL 406
           +FG  +++++I+ P G++
Sbjct: 286 VFGPVLVLLIIFVPDGIV 303


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: 352
Number of extensions: 26
Number of successful extensions: 5
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: 348
Length adjustment: 30
Effective length of query: 387
Effective length of database: 318
Effective search space:   123066
Effective search space used:   123066
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.

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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