GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Limnohabitans curvus MWH-C5

Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate WP_108360184.1 B9Z44_RS12855 amino acid ABC transporter substrate-binding protein

Query= uniprot:Q1MDE9
         (367 letters)



>NCBI__GCF_003063475.1:WP_108360184.1
          Length = 381

 Score =  130 bits (326), Expect = 8e-35
 Identities = 117/372 (31%), Positives = 159/372 (42%), Gaps = 12/372 (3%)

Query: 2   TLKTLTATLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGIL 61
           TLK + A  + +LA    A   I I  I  L+GP    G   KNG + AV EIN  GGIL
Sbjct: 6   TLKAVAAAAIFALAGVAHAQQTIKIANIVELSGPGTTAGTVFKNGVELAVKEINDNGGIL 65

Query: 62  GEKVVLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPT 121
           G+K+     D    P        K V DG+  + GPV SG +I VS   ++ G +     
Sbjct: 66  GKKIENYTVDTQTNPGVAKGLTQKAVDDGVFAIFGPVYSG-SIMVSMAESKRGEVPNFTG 124

Query: 122 ATAPDLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKA 181
             A  +T +G   V RT           AK++  N K K +A++     +GKG  D   A
Sbjct: 125 GEAASITAQGNPYVFRTAFGQSTSFPKLAKFI--NTKAKTLAVIYVNNDFGKGGRDTL-A 181

Query: 182 TLNAGGITEVVNDAIT-PGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAAN 240
            L  G  T+VV D  T  G  DFSA   + K    D ++      E   L R+L      
Sbjct: 182 KLLDGSPTKVVADISTDAGQVDFSAAVLKAKQSNADAIFAYTNEEESARLLRELKKQGWT 241

Query: 241 ATIIGGDGLSNTEFWAIGTDAAGGTI--FTNASDATKSPDSKAAADALAAKNIPAEAFTL 298
             +IG   L+  +   +  DAA G +       DA      K  A    A    ++   +
Sbjct: 242 KPVIGETTLTGQKVIELAGDAANGAMAHVGLTVDAPNPEMLKFKAKYYQAYGSISDHNGI 301

Query: 299 NAYAAVEVLKAGIEKAGSAEDAEAVATALK----DGKEIPTAIGKVTYGETGDLTSQSFS 354
             Y  V VLKA IEK G   D +AVA AL       K+ P  I  V++   GDL  +SF 
Sbjct: 302 KGYTGVYVLKAAIEKVGKL-DRKAVAQALHGINISAKKNPGVIMDVSFDANGDLDRESFL 360

Query: 355 LYKWEAGKIVAA 366
           +      ++V A
Sbjct: 361 IEVKNGRQVVTA 372


Lambda     K      H
   0.312    0.131    0.362 

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: 347
Number of extensions: 23
Number of successful extensions: 4
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: 367
Length of database: 381
Length adjustment: 30
Effective length of query: 337
Effective length of database: 351
Effective search space:   118287
Effective search space used:   118287
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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