GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Sinorhizobium meliloti 1021

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate SMa0711 SMa0711 ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__Smeli:SMa0711
          Length = 276

 Score =  150 bits (380), Expect = 2e-41
 Identities = 91/267 (34%), Positives = 134/267 (50%), Gaps = 6/267 (2%)

Query: 6   LYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRPKFQ- 64
           LY  L ++ G  L P+Y + +TAL   A I       WP  P W +F       RP F  
Sbjct: 11  LYAGLAVVCGVLLFPIYWLFVTALSTLAEIRQLPPSFWPAEPQWSTFAKVGTE-RPIFLW 69

Query: 65  --NSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122
             NS + A+ +  LS +V    GY L+++  +G   L   IL    +P   ++IPLF   
Sbjct: 70  LWNSTLAALGSVALSMVVSVFAGYSLSRFSVKGGRSLGLFILTAKMLPATLLVIPLFGIF 129

Query: 123 KSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILP 182
           +S+GL GSL+ LVL H    IP  T + + Y+  IP EL +AA +DG    G    V+LP
Sbjct: 130 RSMGLIGSLWSLVLAHATLIIPFTTWMLKGYFDTIPRELEQAAMVDGCSPLGALFRVVLP 189

Query: 183 LSVPAFVVVAIWQFTQIWNEFLFAVT-LTRPE-SQPITVALAQLAGGEAVKWNLPMAGAI 240
           ++ P     A++ F   W ++ +A T LT  + S    + +  + G     WN   A A+
Sbjct: 190 VATPGLAATALYAFVLSWADYAYARTFLTNAQGSWTANLGITTMKGEYVTDWNEISAAAV 249

Query: 241 LAALPTLLVYILLGRYFLRGLLAGSVK 267
             ALP +L+Y+ L RY + GL AG+ K
Sbjct: 250 FIALPIILIYLFLERYLVGGLTAGAEK 276


Lambda     K      H
   0.330    0.146    0.461 

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: 260
Number of extensions: 22
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: 268
Length of database: 276
Length adjustment: 25
Effective length of query: 243
Effective length of database: 251
Effective search space:    60993
Effective search space used:    60993
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: 47 (22.7 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