GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Sinorhizobium meliloti 1021

Align ABC transporter permease (characterized, see rationale)
to candidate SMc02472 SMc02472 ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>FitnessBrowser__Smeli:SMc02472
          Length = 312

 Score =  122 bits (306), Expect = 1e-32
 Identities = 86/275 (31%), Positives = 138/275 (50%), Gaps = 14/275 (5%)

Query: 11  PKLVVAPAFVL---GFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVA 67
           P L++   FV+   G A  Y L  WNG  + T        ++ GL  +E L+    +  A
Sbjct: 40  PALLLFTVFVILPMGEAAWYSLYRWNGYGTPT--------QFVGLRNFEVLFNNAAFSRA 91

Query: 68  LKNLGIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLN 127
           L N GI  +  V   + + + LA++L  +I    A R I+  P  L+ V  G  W+++ +
Sbjct: 92  LINNGIIILVSVLLQIPLALWLAMMLAHRIAGVVAFRLIFFLPYVLADVAAGLIWRFVYD 151

Query: 128 PGLGIEKMVRDWGFPNFEFGW-LVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSI 186
              G+   +   GF      + L D  +AIY V+   IW+  GF M LF+AGL+ +D S+
Sbjct: 152 GDYGLVAAIA--GFFGVATPYVLADRSLAIYAVLAVIIWKYFGFHMMLFIAGLQAVDRSV 209

Query: 187 IKAAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVP 246
           ++AA++DGA+  + +  + LP L      ++      +++ FDLVM LT GGP  +T   
Sbjct: 210 LEAAEIDGATGWQKFRYVTLPLLGSTVRLSIFFAVIGSLQLFDLVMPLTGGGPSNSTQTM 269

Query: 247 ATFMYTMSFSRGQIGLGAASATMMLATVAALVIPY 281
            TF+YT   +R Q+GLG+A   ++      L   Y
Sbjct: 270 VTFLYTYGVTRMQVGLGSAVGVVLFVICVTLAFGY 304


Lambda     K      H
   0.327    0.141    0.451 

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: 258
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: 293
Length of database: 312
Length adjustment: 27
Effective length of query: 266
Effective length of database: 285
Effective search space:    75810
Effective search space used:    75810
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 (21.7 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