GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ 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_023430731.1 N177_RS02905 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_000496075.1:WP_023430731.1
          Length = 375

 Score =  160 bits (406), Expect = 4e-44
 Identities = 116/355 (32%), Positives = 176/355 (49%), Gaps = 11/355 (3%)

Query: 3   KGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINK 62
           +G +  +   AA+   G A    A +T+KI   GP++G  +Q G   R G  +AI+Q N 
Sbjct: 9   RGARVAAIALAAVVATGAAD---AQETVKIGFIGPLSGGNSQQGLTARNGFQLAIDQANA 65

Query: 63  AGGVNGAQLEGVIYDDACDPKQAVAVANKVVND-GVKFVVGHVCSSSTQPATDIYEDEGV 121
              + G ++EGVI DDA +P+  V+ A K+ ND  V  V GH  S        +    G+
Sbjct: 66  REDL-GFKIEGVIQDDASNPQTGVSAALKLTNDPAVIAVTGHWNSPVALATAPVITRAGI 124

Query: 122 LMITPSATAPEITSRGYKLIFRTIG-LDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEG 180
             +   A +P+IT     L+ R +  L N   P+A  + AE    + IA++ D   YG  
Sbjct: 125 PFVIWGAISPKITETNNPLLARVVPTLVNTNEPLAA-WAAEEI-GQNIAIVSDTSDYGMA 182

Query: 181 IATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQA 240
                +K  E+AG  +   E    G  DF A ++K+K      +YFGG   E GL+ +Q 
Sbjct: 183 NVAAFRKPFEEAGGTITSVETAPVGTTDFRATLTKIKSDNPDAIYFGGVVTEAGLVRQQM 242

Query: 241 KQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKN-QDP 299
           K+ GLD   +G +G  + E   IAGDA+EG ++ + +  E + K   + +A+ A    +P
Sbjct: 243 KEVGLDVPMIGVDGFHDPEFIKIAGDAAEGTISGIMKETENE-KLVEMNEAYAAAGFAEP 301

Query: 300 SGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLK 354
            G +   AY A  +I   IE+AG  D   V EA+RA  ++   G+  FDE G  K
Sbjct: 302 VGTYTKNAYDAANIIIAAIEEAG-TDRAAVGEAIRAMEYDGAMGHTSFDENGQTK 355


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: 321
Number of extensions: 14
Number of successful extensions: 5
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