GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Pantoea rwandensis LMG 26275

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_084936137.1 HA51_RS18910 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_002095475.1:WP_084936137.1
          Length = 375

 Score =  430 bits (1106), Expect = e-125
 Identities = 212/369 (57%), Positives = 275/369 (74%), Gaps = 5/369 (1%)

Query: 10  RLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGA 69
           R   A  +A   S++  A  IKIA+ G  TGPVAQYGDMQ  GA  AI+ IN  GGVNG 
Sbjct: 7   RALLAGCVALALSHAALAKDIKIAIVGAATGPVAQYGDMQFTGAAQAIKDINAKGGVNGD 66

Query: 70  QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129
           +L GV YDDACDPKQAVAVANKVVNDG+K+V+GH+CSSSTQPA+DIY DEG+LMITP+AT
Sbjct: 67  KLVGVEYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYNDEGILMITPAAT 126

Query: 130 APEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTV 189
           APE+T+RGY  + RT GLD+ QGP A  +I    K K IAV+HDKQQYG+G+A  V+KT+
Sbjct: 127 APELTARGYADVLRTTGLDSDQGPTAATYILNEIKPKRIAVVHDKQQYGQGLAESVQKTL 186

Query: 190 EDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARF 249
           +  G  V +FEG+ AGDKDF+ LI++LKK  V FVY+GGY+PE+G +LRQAK AGL+A F
Sbjct: 187 KAKGGNVVLFEGITAGDKDFSTLIARLKKENVDFVYYGGYYPELGQILRQAKAAGLNAGF 246

Query: 250 MGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKA----KNQDPSGIFVL 305
           MGPEGVGN+ ++ IAGDASEG+  TLP+ ++Q P+NKA+++A KA      +DP+G FV 
Sbjct: 247 MGPEGVGNASLSNIAGDASEGLYVTLPKRYDQLPENKAIVEAIKANTASNRKDPTGPFVW 306

Query: 306 PAYSAVTVIAKGIEKAGEADPEKVAEALRAN-TFETPTGNLGFDEKGDLKNFDFTVYEWH 364
             Y+A+  +  GIE++  A+P+ +A+ L+      T  GNL +D+KGDLK F+F V++WH
Sbjct: 307 TTYAAIQSLVAGIERSKSAEPDAIAKNLKEGAAVPTVMGNLNWDQKGDLKGFEFGVFKWH 366

Query: 365 KDATRTEVK 373
           KD + T VK
Sbjct: 367 KDGSSTAVK 375


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: 482
Number of extensions: 19
Number of successful extensions: 3
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: 375
Length adjustment: 30
Effective length of query: 343
Effective length of database: 345
Effective search space:   118335
Effective search space used:   118335
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