GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Azospirillum thiophilum BV-S

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_045585665.1 AL072_RS27965 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_001305595.1:WP_045585665.1
          Length = 376

 Score =  291 bits (746), Expect = 2e-83
 Identities = 154/362 (42%), Positives = 227/362 (62%), Gaps = 10/362 (2%)

Query: 7   RLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGV 66
           R + L   +++A     + AAD +K+ LAGPVTG  A + +  R GA +A+  +N AGG+
Sbjct: 13  RSNLLRFGISLAALVPTAAAAD-VKLGLAGPVTGQYASFMEQMRRGADLAVADLNAAGGI 71

Query: 67  NGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITP 126
           NG ++   + DDACDPKQAVAVAN+ V DGV+ VVGH CSSST PA+ +Y + G++++TP
Sbjct: 72  NGEKVVLQVADDACDPKQAVAVANRFVADGVQAVVGHFCSSSTIPASSVYAESGLVIVTP 131

Query: 127 SATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVK 186
           ++T P IT RG   +FR  G D+    VA K I  R   +TIA++HDK  YG+GIA  V+
Sbjct: 132 ASTNPTITERGLTNMFRVCGRDDQAAGVAAKQIVGRNLGRTIAIVHDKSTYGQGIAEGVR 191

Query: 187 KTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLD 246
             +   G  V +FEG+  G++DF++L++++K   V  V+FGGYH E GLL+RQA + GL 
Sbjct: 192 TELAQQGRNVVLFEGITQGERDFSSLVARMKALNVDVVFFGGYHTEAGLLVRQASEQGLK 251

Query: 247 ARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKA----LIDAFKAKNQDPSGI 302
            RF+  +G+  +E  +IAG AS+G++ T    F  DP+  A    L+  F+    +P G 
Sbjct: 252 TRFVAGDGLATTEFASIAGPASDGVMFT----FYPDPRANAGTADLVRRFRTAGFEPEG- 306

Query: 303 FVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYE 362
           F L  Y+AV V+A   + A     +++A+ALRA T+ T  G++ FD KGD  +  F +Y 
Sbjct: 307 FTLYTYAAVRVLADAAKAAKTMKGDRLADALRAGTYHTVLGDIRFDRKGDPNSEPFVLYA 366

Query: 363 WH 364
           W+
Sbjct: 367 WN 368


Lambda     K      H
   0.316    0.133    0.377 

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: 374
Number of extensions: 16
Number of successful extensions: 2
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: 373
Length of database: 376
Length adjustment: 30
Effective length of query: 343
Effective length of database: 346
Effective search space:   118678
Effective search space used:   118678
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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