GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudomonas putida KT2440

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate PP_0618 PP_0618 Branched-chain amino acid ABC transporter, permease protein

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__Putida:PP_0618
          Length = 286

 Score =  160 bits (405), Expect = 3e-44
 Identities = 94/295 (31%), Positives = 168/295 (56%), Gaps = 20/295 (6%)

Query: 1   MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60
           ++L L QL+NGL LG +Y L+A+G T+++G++  +NFAHG  +++GA++ Y  + +   N
Sbjct: 2   LDLYLFQLLNGLGLGMIYFLIAVGLTIIFGLLNFVNFAHGAFFLLGAYLCYTAV-AVTGN 60

Query: 61  FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYL---VGAN 117
           F++AL++A L  A L   +E L  + + H      ++  +G++ +++   V +   VG N
Sbjct: 61  FWLALLIAPLVVAALAWAVERLLIKRIYHLPHTFQILVTLGIALIIQEASVLIWGPVGKN 120

Query: 118 TRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDA 177
             A P  ++ V   LG       +L ++G + ++ I L +++++T+ G  +RA S  ++ 
Sbjct: 121 I-AVPPELRGVLI-LGDFIYPYYRLFLIGFAALIGIGLWLLLERTRFGALVRAGSESTET 178

Query: 178 AQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLK------SFVAAV 231
             L+G N+ R  S TFALG  LAG AGVL A       PL G  P +       +FV  V
Sbjct: 179 VSLLGTNIFRLFSLTFALGVGLAGVAGVLFA-------PLRGAQPFVGPEILGIAFVVVV 231

Query: 232 LGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286
           +GG+G   GA +GG ++G++++  T+         ++YG +  +++VRP G+ G+
Sbjct: 232 IGGMGSFGGALVGGLLVGVVQSMMTSL-WPQGASLMIYGAMAAVILVRPYGLFGR 285


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: 246
Number of extensions: 12
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: 292
Length of database: 286
Length adjustment: 26
Effective length of query: 266
Effective length of database: 260
Effective search space:    69160
Effective search space used:    69160
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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