GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manY in Klebsiella michiganensis M5al

Align mannose permease IIC component (characterized)
to candidate BWI76_RS17895 BWI76_RS17895 PTS mannose/fructose/sorbose transporter subunit IIC

Query= CharProtDB::CH_088330
         (266 letters)



>FitnessBrowser__Koxy:BWI76_RS17895
          Length = 266

 Score =  488 bits (1256), Expect = e-143
 Identities = 251/266 (94%), Positives = 261/266 (98%)

Query: 1   MEITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIA 60
           MEIT LQIVLVFIVACIAGM S+LDEFQFHRPL+ACTL+G VLGDMKTGIIIGGTLEMIA
Sbjct: 1   MEITLLQIVLVFIVACIAGMESVLDEFQFHRPLVACTLIGAVLGDMKTGIIIGGTLEMIA 60

Query: 61  LGWMNIGAAVAPDAALASIISTILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF 120
           LGWMNIGAAVAPDAALASIIST+LVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF
Sbjct: 61  LGWMNIGAAVAPDAALASIISTVLVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF 120

Query: 121 QHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEVVTN 180
           QHAADKAA+NGNLTAISW+HVSSLFLQAMR+AIPAVIVA+SVGTSEVQ +LNAIPEVVT 
Sbjct: 121 QHAADKAAENGNLTAISWLHVSSLFLQAMRIAIPAVIVAISVGTSEVQGLLNAIPEVVTG 180

Query: 181 GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVLYIQ 240
           GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFT+FNLVALGVIGTVMAVLYIQ
Sbjct: 181 GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTDFNLVALGVIGTVMAVLYIQ 240

Query: 241 LSPKYNRVAGAPAQAAGNNDLDNELD 266
           LSPKYNRVAGAPAQAAGNNDLDNELD
Sbjct: 241 LSPKYNRVAGAPAQAAGNNDLDNELD 266


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: 361
Number of extensions: 3
Number of successful extensions: 1
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: 266
Length adjustment: 25
Effective length of query: 241
Effective length of database: 241
Effective search space:    58081
Effective search space used:    58081
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 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