GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Acidovorax sp. GW101-3H11

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Ac3H11_1432 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1432
          Length = 294

 Score =  166 bits (419), Expect = 8e-46
 Identities = 93/285 (32%), Positives = 168/285 (58%), Gaps = 5/285 (1%)

Query: 4   MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFV 63
           +L QL+ GL+ GS YA+L+LG  +++G++ +INFAHG ++M GA I +  +N   +N+++
Sbjct: 11  LLSQLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMTGALITWMAMNYLGINYWL 70

Query: 64  ALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLE--YGMVYLVGANTRAF 121
            L++A L   + GV+IE L  R +     +  L+  +G++ L+E  +  +Y V       
Sbjct: 71  MLVLAPLVVGLFGVLIERLLLRWIYKLDHLYGLLLTLGLTLLIEGVFRSIYGVSGLGYDT 130

Query: 122 PQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLM 181
           P+ ++    +LG + + N +  ++  S+++ +    +++KTK+G  +RA + +    +  
Sbjct: 131 PELLEGAT-NLGFMIMPNYRAWVVVASIVVCVATWYVIEKTKLGAYLRAGTENPRLVEAF 189

Query: 182 GINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGA 241
           GINV   ++ T+A G+ALA  AGVL A  Y  + PLMG    +  F   V+GG+G I G+
Sbjct: 190 GINVPVMVTLTYAFGAALAAFAGVLAAPVY-QVTPLMGQNLIIVVFAVVVIGGMGSIMGS 248

Query: 242 ALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286
            L G  +G++E F   F   +    +V+ I++++L++RPAG+ GK
Sbjct: 249 ILTGLGLGVIEGFTKVF-YPEASSTVVFVIMVIVLLIRPAGLFGK 292


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: 240
Number of extensions: 13
Number of successful extensions: 3
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: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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.

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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