GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Dinoroseobacter shibae DFL-12

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__Dino:3607448
          Length = 305

 Score =  140 bits (352), Expect = 5e-38
 Identities = 94/308 (30%), Positives = 159/308 (51%), Gaps = 30/308 (9%)

Query: 3   LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62
           L+++Q++NGL  G +  L+A G T+V+G++ LIN AHG +YM+GAF    +  +   +F 
Sbjct: 5   LLIEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAVAGA-TGSFV 63

Query: 63  VALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFP 122
           + L  A+ A A  G +IE    R L     +  ++    +  +   G  ++ G    +FP
Sbjct: 64  LGLAAALAAAAAAGALIEVTIIRRLYARDHLDQVLATFALILIFSEGTRWIFG----SFP 119

Query: 123 QAIQTVRYDLGPISL------TNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSD 176
             ++      GP++L         +L I+GI L +   L  ++ KT++G  +RA   D +
Sbjct: 120 LFLEVPAALSGPVTLPFGIEYPAYRLAIIGIGLAIAAALFWLIAKTRIGVQIRAGEADRE 179

Query: 177 AAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIG 236
               +G++++R  +  FALG+ALAG AG L+     S++  MG    + +FV  V+GGIG
Sbjct: 180 MIAALGVDIDRLYTLVFALGAALAGLAGALVGA-LQSVQVGMGEPVLILAFVVIVIGGIG 238

Query: 237 IIPGAALGGFVIGLLET-----------------FATAFGMSDFRDAIVYGILLLILIVR 279
            I GA +G  ++GL +T                  ATA G S      +Y ++  +LI R
Sbjct: 239 SIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVG-SALASMAIYILMAGVLIFR 297

Query: 280 PAGILGKN 287
           P+G+ G++
Sbjct: 298 PSGLFGQS 305


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: 213
Number of extensions: 12
Number of successful extensions: 2
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: 305
Length adjustment: 27
Effective length of query: 265
Effective length of database: 278
Effective search space:    73670
Effective search space used:    73670
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