GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Klebsiella michiganensis M5al

Align ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS07280 BWI76_RS07280 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS07280
          Length = 316

 Score =  357 bits (917), Expect = e-103
 Identities = 183/316 (57%), Positives = 237/316 (75%), Gaps = 7/316 (2%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MD L+QQIING++LGS+YALIALGYTMVYGI+++INFAHG++LM+GALT+ S +  +   
Sbjct: 1   MDTLIQQIINGVMLGSIYALIALGYTMVYGILRIINFAHGDILMVGALTTLSGMHALNAH 60

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
            P  P    L LA ++A  V A L   +E+ AYR LR++PRLAPLI+ IG+S+LLQT+AM
Sbjct: 61  FPTLPPLAQLGLALLLAMTVCALLAMAVERFAYRRLRNAPRLAPLISGIGVSVLLQTVAM 120

Query: 121 IIWKPNYKPYPTMLPSSPFEI--GGAFITPTQILILGVTAVALASLVYL-----VNHTNL 173
           I+W  N   +P +LP  P  +  G A   P  I + G+  VALA  V L     V +T L
Sbjct: 121 IVWSRNPLMFPQILPMDPIAVTHGSAAHPPALITVTGIVTVALALTVMLGLWLLVEYTRL 180

Query: 174 GRAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGL 233
           GR MRA AENPR+A+LMGV P+ +I+ TF IG V AA+AG+M ASNYG+A  +MGFLPG+
Sbjct: 181 GRGMRAVAENPRIATLMGVNPNAIIALTFAIGGVFAALAGVMMASNYGSAGFSMGFLPGI 240

Query: 234 KAFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIIL 293
           KAFTAAV GGIGN+ GA++GG+LLGLIE++G+GY+G LT G+ GS+Y DIFAF+VLI++L
Sbjct: 241 KAFTAAVLGGIGNIRGAMIGGLLLGLIESLGAGYLGDLTHGVFGSNYQDIFAFMVLILVL 300

Query: 294 TLRPSGLLGERVADRA 309
             RP+GLLGERVA RA
Sbjct: 301 VFRPAGLLGERVAHRA 316


Lambda     K      H
   0.327    0.142    0.419 

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: 282
Number of extensions: 7
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: 309
Length of database: 316
Length adjustment: 27
Effective length of query: 282
Effective length of database: 289
Effective search space:    81498
Effective search space used:    81498
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