GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Herbaspirillum aquaticum IEH 4430

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_088755661.1 CEJ45_RS13770 ATP-binding cassette domain-containing protein

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_002213425.1:WP_088755661.1
          Length = 859

 Score =  194 bits (493), Expect = 9e-54
 Identities = 104/287 (36%), Positives = 160/287 (55%), Gaps = 25/287 (8%)

Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179
           I +  ++GIGLN+++GL G +  G+VGFYAVGAYT A+L       FW A P+A ++A  
Sbjct: 65  IALVAIVGIGLNVLIGLTGQVSFGHVGFYAVGAYTVAILTTKVQLSFWLAWPLAAVVAGA 124

Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239
            G LL  P LR++G YLA++T+ F  II+  +  + ++TGG NGI  +  P   GL  ER
Sbjct: 125 LGVLLALPALRVKGPYLAMITIAFSFIIQHAIIELRDLTGGQNGIMGLAAPAFLGLQAER 184

Query: 240 RAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDE 299
                                    + V+ L+   + L     L R   G A  A+R+ E
Sbjct: 185 ------------------------AIAVLGLITAAVVLAAYCWLSRGSWGAAMRAVRDSE 220

Query: 300 VACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGG 359
            A  ++GLNP ++K  AF + A+ AG AG  FA     VTP++F+F++S + + +VVLGG
Sbjct: 221 TAAESIGLNPLVIKTVAFALSAALAGLAGGLFAPLSTFVTPDTFSFMQSILFVLVVVLGG 280

Query: 360 MGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGL 405
            GS LG ++ AV++  L E +    +YR+L FG  +++++   P G+
Sbjct: 281 SGSILGPVIGAVIVGALPELLSSLEDYRLLFFGALLLLVLWVAPDGV 327


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: 837
Number of extensions: 38
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 859
Length adjustment: 37
Effective length of query: 380
Effective length of database: 822
Effective search space:   312360
Effective search space used:   312360
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: 53 (25.0 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