GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manY in Weissella oryzae SG25

Align mannose permease IIC component (characterized)
to candidate WP_027699770.1 TT13_RS09610 mannose/fructose/sorbose family PTS transporter subunit IIC

Query= CharProtDB::CH_088330
         (266 letters)



>NCBI__GCF_000691805.2:WP_027699770.1
          Length = 270

 Score =  215 bits (547), Expect = 9e-61
 Identities = 113/244 (46%), Positives = 165/244 (67%), Gaps = 6/244 (2%)

Query: 3   ITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIALG 62
           ++ + +  V I A +AG+  ILD++Q H+P+IA +L+G+  G +  GII+GG L++IALG
Sbjct: 1   MSAISVFFVLIFAFLAGLEGILDQWQLHQPIIASSLIGLATGHLAAGIILGGFLQLIALG 60

Query: 63  WMNIGAAVAPDAALASIISTILVI-AGHQSI----GAGIALAIPLAAAGQVLTIIVRTIT 117
           W N+GAAVAPDAALAS+ S IL++ +G+ S+    G  I  AI LA AG VLT +VR  +
Sbjct: 61  WANVGAAVAPDAALASVASAILMVQSGNFSVENIKGIIIPAAILLATAGLVLTTLVRFFS 120

Query: 118 VAFQHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEV 177
           VA  H AD  A+ G+   +++ H+ +L +Q +R+AIPA ++ L V    V + L +IP V
Sbjct: 121 VAIVHLADAQAEKGSYRGVAFWHIVALVMQGLRIAIPAGLL-LIVPQQVVMHALQSIPPV 179

Query: 178 VTNGLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVL 237
           ++ GL I GGM+VVVGY MVIN+M    L PFF+LGF  A      L+A+G+IG V+A++
Sbjct: 180 ISGGLTIGGGMVVVVGYGMVINLMATRELWPFFFLGFAIAPINQLTLIAIGIIGVVIALV 239

Query: 238 YIQL 241
           Y+ L
Sbjct: 240 YLTL 243


Lambda     K      H
   0.326    0.139    0.397 

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: 237
Number of extensions: 11
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: 266
Length of database: 270
Length adjustment: 25
Effective length of query: 241
Effective length of database: 245
Effective search space:    59045
Effective search space used:    59045
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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