GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manX in Klebsiella michiganensis M5al

Align PTS system, mannose-specific, IIAB component, component of The primary glucose /mannose uptake transporter, ManLMN (characterized)
to candidate BWI76_RS01735 BWI76_RS01735 PTS mannose/fructose/sorbose family transporter subunit IIB

Query= TCDB::E1UCI0
         (321 letters)



>FitnessBrowser__Koxy:BWI76_RS01735
          Length = 164

 Score =  137 bits (344), Expect = 2e-37
 Identities = 65/164 (39%), Positives = 105/164 (64%), Gaps = 1/164 (0%)

Query: 155 IEFVLTRVDSRLLHGQVATAWTKATHPTRIIVVSDAVAKDDLRKKLIEQAAPPGVKANVI 214
           +   L R+D RL+HGQV T W+K  +  RII+ +D V  DD+R+ L+ QAAPPG+K NV+
Sbjct: 1   MNITLARIDDRLIHGQVTTVWSKVANAQRIIICNDDVYNDDVRRTLLRQAAPPGMKVNVV 60

Query: 215 PVQKMIEISKDPRFGNTKALLLFENPQDVLRAIEGGVEIEQVNVGSMAHSVGKVVVSKVL 274
            ++K + +  +P++ +     LF NPQDVL  ++ GV I  +N+G MA   GK  ++K +
Sbjct: 61  NLEKAVAVYHNPQYQDETVFYLFTNPQDVLTMVQQGVNIATLNIGGMAWRPGKKQLTKAV 120

Query: 275 SMGKDDVATFEKLKEKGVKFDVRKVPNDSSAN-MDEIIKKAKNE 317
           S+ + D+  F++L + GV  D+R V +D S N +D+I +++  E
Sbjct: 121 SLDEADINAFQQLDKLGVNLDLRVVASDPSVNILDKIAEQSVTE 164


Lambda     K      H
   0.315    0.132    0.365 

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: 126
Number of extensions: 1
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: 321
Length of database: 164
Length adjustment: 23
Effective length of query: 298
Effective length of database: 141
Effective search space:    42018
Effective search space used:    42018
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 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