GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00870 in Lutibaculum baratangense AMV1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_023434291.1 N177_RS20180 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>NCBI__GCF_000496075.1:WP_023434291.1
          Length = 369

 Score =  163 bits (413), Expect = 6e-45
 Identities = 116/370 (31%), Positives = 179/370 (48%), Gaps = 24/370 (6%)

Query: 9   VVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKK 68
           V+  +AAA G A A+   + I    P++G  A +G   + GA  A++++NA G  +G + 
Sbjct: 10  VLVGLAAAPGAALAE---IAIATAGPMTGQYATFGAQMKAGAEQAVKDINAAGGVLGEQL 66

Query: 69  IKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAA 128
           +   L   DDA DPKQ  A A +     V  V GH  SG++IPAS+VY + GI  ++ A+
Sbjct: 67  V---LRIGDDACDPKQAVAVANQFAGGDVVFVAGHFCSGSSIPASQVYAEEGIIQISPAS 123

Query: 129 TNPNLT--KPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFK 186
           TNP  T  +PG    FR+   D+  G     Y  +    K +AI+ D+TAYG+G+AD  K
Sbjct: 124 TNPTFTENRPG-DGIFRVCGRDDQQGQVAGEYLAEHFGDKNIAIVHDKTAYGKGLADETK 182

Query: 187 KTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMG 246
           K     G + V  +  T    D+ A+++ +K  N D ++ GG   + G ++RQM   GM 
Sbjct: 183 KYLNEAGKEEVIYEAYTAGEKDYTALVSKLKQSNVDVLYVGGYHTEAGLIVRQMRDQGMD 242

Query: 247 NVKYFGGDGICTSEIAKLA--AGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304
            +    GD + T E   +   AGA TL          + +  P  +   A    ++  Q 
Sbjct: 243 TI-LVSGDALVTDEYWSITGDAGAGTL---------MTFSPDPRKSEKAAPVVEEFRGQN 292

Query: 305 ---QVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPA 361
              + Y  YTY A    V A++ A S D       L + +F  V   + F+  G++  P 
Sbjct: 293 IEPEGYVLYTYAAIQAWVQAVEAAGSTDYDAVVDALNEGTFDTVLGELEFDDKGDVTLPG 352

Query: 362 ITLYVYKDGK 371
              Y +KDG+
Sbjct: 353 YVFYEWKDGE 362


Lambda     K      H
   0.315    0.131    0.375 

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: 359
Number of extensions: 19
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: 375
Length of database: 369
Length adjustment: 30
Effective length of query: 345
Effective length of database: 339
Effective search space:   116955
Effective search space used:   116955
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: 42 (22.0 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