GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Brucella inopinata BO1

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_008507466.1 BIBO1_RS12220 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_000182725.1:WP_008507466.1
          Length = 371

 Score =  288 bits (737), Expect = 2e-82
 Identities = 148/337 (43%), Positives = 208/337 (61%), Gaps = 2/337 (0%)

Query: 30  IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQLEGVIYDDACDPKQAVAVA 89
           I + +  P+TG  A +G+  + G   A+ + N  GG+NG Q+  V  DDA DPKQ ++VA
Sbjct: 25  IMVGVGAPLTGSQAAFGEQIKRGVEAAVAEANAKGGMNGEQITLVYGDDAADPKQGISVA 84

Query: 90  NKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTIGLDN 149
           NK V DGVKFV+GH  S  + P +DIY + GVLMI P  T P  T R     FRT   D+
Sbjct: 85  NKFVGDGVKFVIGHFNSGVSIPTSDIYAENGVLMIAPGTTNPTFTERELWNTFRTCRRDD 144

Query: 150 MQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAGDKDF 209
            QG VAGK++A+ YKD  +A+LHDK  YG+G+A E KK++ + G+K  ++EG+N GDKDF
Sbjct: 145 KQGIVAGKYMADNYKDGKVAILHDKTPYGQGLADETKKSLNENGMKETLYEGVNQGDKDF 204

Query: 210 NALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAGDASE 269
           +ALISK+K AG+  VY+GG HPE GLL+RQ    GL A+F+  +G+ ++E+ +IAGDA  
Sbjct: 205 SALISKMKAAGITAVYWGGMHPEAGLLIRQMADQGLKAQFISGDGIVSNELASIAGDAVA 264

Query: 270 GMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEADPEKV 329
           G++ T       D  N  LI AF+ K  +P   +   AY+ V  +      AG  DP +V
Sbjct: 265 GVMNTFGPDPRDDKANAELIKAFRDKGFEPEA-YTFYAYAGVQSLVNAANAAGSNDPMEV 323

Query: 330 AEALR-ANTFETPTGNLGFDEKGDLKNFDFTVYEWHK 365
           A A++    F+T  G++ FD KGD     + ++EW K
Sbjct: 324 ATAMKEKGPFKTVLGDISFDAKGDPSLSPYVMFEWRK 360


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: 434
Number of extensions: 17
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: 371
Length adjustment: 30
Effective length of query: 343
Effective length of database: 341
Effective search space:   116963
Effective search space used:   116963
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: 49 (23.5 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