GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Lutibaculum baratangense AMV1

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_023434291.1 N177_RS20180 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_000496075.1:WP_023434291.1
          Length = 369

 Score =  288 bits (736), Expect = 2e-82
 Identities = 152/355 (42%), Positives = 217/355 (61%), Gaps = 3/355 (0%)

Query: 11  LFAAMAIAGFASYSMAA-DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGA 69
           L A + + G A+   AA   I IA AGP+TG  A +G   +AGA  A++ IN AGGV G 
Sbjct: 5   LLAGVVLVGLAAAPGAALAEIAIATAGPMTGQYATFGAQMKAGAEQAVKDINAAGGVLGE 64

Query: 70  QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129
           QL   I DDACDPKQAVAVAN+     V FV GH CS S+ PA+ +Y +EG++ I+P++T
Sbjct: 65  QLVLRIGDDACDPKQAVAVANQFAGGDVVFVAGHFCSGSSIPASQVYAEEGIIQISPAST 124

Query: 130 APEIT-SRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188
            P  T +R    IFR  G D+ QG VAG+++AE + DK IA++HDK  YG+G+A E KK 
Sbjct: 125 NPTFTENRPGDGIFRVCGRDDQQGQVAGEYLAEHFGDKNIAIVHDKTAYGKGLADETKKY 184

Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248
           + +AG +  ++E   AG+KD+ AL+SKLK++ V  +Y GGYH E GL++RQ +  G+D  
Sbjct: 185 LNEAGKEEVIYEAYTAGEKDYTALVSKLKQSNVDVLYVGGYHTEAGLIVRQMRDQGMDTI 244

Query: 249 FMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAY 308
            +  + +   E  +I GDA  G L T      +  K   +++ F+ +N +P G +VL  Y
Sbjct: 245 LVSGDALVTDEYWSITGDAGAGTLMTFSPDPRKSEKAAPVVEEFRGQNIEPEG-YVLYTY 303

Query: 309 SAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363
           +A+    + +E AG  D + V +AL   TF+T  G L FD+KGD+    +  YEW
Sbjct: 304 AAIQAWVQAVEAAGSTDYDAVVDALNEGTFDTVLGELEFDDKGDVTLPGYVFYEW 358


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: 389
Number of extensions: 15
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: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
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