GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Frankia alni ACN14a

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 WP_041938756.1 FRAAL_RS03130 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_000058485.1:WP_041938756.1
          Length = 515

 Score =  223 bits (568), Expect = 1e-62
 Identities = 134/335 (40%), Positives = 190/335 (56%), Gaps = 34/335 (10%)

Query: 96  LALVVVAFVWPFFASRGAVD-IATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYT 154
           L L+ VA + P   S  A   +   I IY +L +GLN+VVG AGLLDLGY+ F+A+GAY 
Sbjct: 180 LVLLAVAILAPLVVSTAAQQSMVNDIGIYALLALGLNVVVGYAGLLDLGYIAFFAIGAYA 239

Query: 155 YALLAEYAGFGF--------WTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEI 206
            A         +        +   PIA ++AAL G +LG P LRLRGDYLAIVTLGFGEI
Sbjct: 240 TAYFTSQTAMPWHAPFVLNPFFVFPIALVLAALAGVILGAPTLRLRGDYLAIVTLGFGEI 299

Query: 207 IRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLY 266
           I ++  N   IT G  G   +P  ++                 +  GI Y      +  Y
Sbjct: 300 IHLVANNADGITNGARGAFGVPHLSI-----------------DLLGIDYKWGIDPLPYY 342

Query: 267 VVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGF 326
            + L +V+  +    RL R  IGR+W A+REDE+A  A G+    +KL AF IGAS +GF
Sbjct: 343 YLLLAIVIGVMIAFGRLERSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAIGASVSGF 402

Query: 327 AGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVM-----VLLQEMRG 381
           AG  FA++Q    P+SF+   S  ++A+V+ GGMGS+LGV++ AVV+      L  +++ 
Sbjct: 403 AGVLFASKQ-FFNPQSFSLQASFFVVAVVIFGGMGSRLGVVVGAVVLQGLAFYLRDKVQP 461

Query: 382 FNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
            + Y  + FG  +++MMI+RPQGL+P +R   E++
Sbjct: 462 ADRY--IYFGAVIVIMMIFRPQGLVPSRRRRREIE 494


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: 617
Number of extensions: 24
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: 515
Length adjustment: 33
Effective length of query: 384
Effective length of database: 482
Effective search space:   185088
Effective search space used:   185088
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 Apr 09 2024. 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