GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Streptococcus massiliensis 4401825

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_018371595.1 BN415_RS07285 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQI0
         (292 letters)



>NCBI__GCF_000341525.1:WP_018371595.1
          Length = 289

 Score =  472 bits (1214), Expect = e-138
 Identities = 239/289 (82%), Positives = 270/289 (93%)

Query: 4   MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFV 63
           MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAF+GY+LI S  MNF++
Sbjct: 1   MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFMGYYLIGSLHMNFYL 60

Query: 64  ALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFPQ 123
           ALIV+M+ TA LGV+IEFLAYRPLRHSTRIA LITAIGVSF LEY MV +V AN +AFPQ
Sbjct: 61  ALIVSMVGTAALGVLIEFLAYRPLRHSTRIAALITAIGVSFFLEYSMVAVVSANVKAFPQ 120

Query: 124 AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGI 183
            + +VR+ LGP+S+T++QL IL ++LILM+LLQ+IVQKTKMGKAMRAVSVDSDAAQLMGI
Sbjct: 121 VLPSVRFVLGPVSVTSIQLTILAVALILMVLLQLIVQKTKMGKAMRAVSVDSDAAQLMGI 180

Query: 184 NVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAAL 243
           NVN+TISFTFALGSALAGAAGVLIALYYNSL+PLMG+TPGLKSFVAAV+GGIGIIPGAAL
Sbjct: 181 NVNQTISFTFALGSALAGAAGVLIALYYNSLDPLMGMTPGLKSFVAAVIGGIGIIPGAAL 240

Query: 244 GGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292
           GGFVIG+LETFAT   +S++RDAIVYGIL+LIL++RPAGILGKNVKEKV
Sbjct: 241 GGFVIGILETFATVINLSEYRDAIVYGILILILLIRPAGILGKNVKEKV 289


Lambda     K      H
   0.330    0.146    0.407 

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: 354
Number of extensions: 17
Number of successful extensions: 1
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: 292
Length of database: 289
Length adjustment: 26
Effective length of query: 266
Effective length of database: 263
Effective search space:    69958
Effective search space used:    69958
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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