GapMind for catabolism of small carbon sources

 

Alignments for a candidate for levF in Cronobacter condimenti 1330

Align mannose permease IIC component (characterized)
to candidate WP_007668609.1 BN137_RS13780 PTS mannose/fructose/sorbose transporter subunit IIC

Query= CharProtDB::CH_088330
         (266 letters)



>NCBI__GCF_000319285.1:WP_007668609.1
          Length = 266

 Score =  478 bits (1230), Expect = e-140
 Identities = 249/266 (93%), Positives = 256/266 (96%)

Query: 1   MEITTLQIVLVFIVACIAGMGSILDEFQFHRPLIACTLVGIVLGDMKTGIIIGGTLEMIA 60
           MEITTLQIVLVFIVACIAGM S+LDEFQFHRPL+ACTLVG VLGDMKTGIIIGGTLEMIA
Sbjct: 1   MEITTLQIVLVFIVACIAGMESVLDEFQFHRPLVACTLVGAVLGDMKTGIIIGGTLEMIA 60

Query: 61  LGWMNIGAAVAPDAALASIISTILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVAF 120
           LGWMNIGAAVAPDAALASIIS ILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITV F
Sbjct: 61  LGWMNIGAAVAPDAALASIISAILVIAGHQSIGAGIALAIPLAAAGQVLTIIVRTITVGF 120

Query: 121 QHAADKAADNGNLTAISWIHVSSLFLQAMRVAIPAVIVALSVGTSEVQNMLNAIPEVVTN 180
           QHAADKAA NGNLTA+SWIHVSSLFLQAMR+AIPAVIVA+SVGTSEVQ+MLNAIPEVVT 
Sbjct: 121 QHAADKAALNGNLTALSWIHVSSLFLQAMRIAIPAVIVAISVGTSEVQSMLNAIPEVVTG 180

Query: 181 GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTNFNLVALGVIGTVMAVLYIQ 240
           GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFT+FNLVALGVIG VMAVLYIQ
Sbjct: 181 GLNIAGGMIVVVGYAMVINMMRAGYLMPFFYLGFVTAAFTDFNLVALGVIGAVMAVLYIQ 240

Query: 241 LSPKYNRVAGAPAQAAGNNDLDNELD 266
           LSPKYNR AGAPAQ AG NDLDNELD
Sbjct: 241 LSPKYNRSAGAPAQTAGANDLDNELD 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: 347
Number of extensions: 4
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 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