GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Limnohabitans curvus MWH-C5

Align ABC transporter permease (characterized, see rationale)
to candidate WP_108358422.1 B9Z44_RS05730 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>NCBI__GCF_003063475.1:WP_108358422.1
          Length = 305

 Score =  178 bits (451), Expect = 2e-49
 Identities = 102/314 (32%), Positives = 175/314 (55%), Gaps = 16/314 (5%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQG- 59
           M  +LQ +++GL LG +YAL+A+G+ + +   +  NF  GE L +G + + S + ++ G 
Sbjct: 1   MVAILQALLSGLALGGIYALVAVGFNITHNTTKTFNFGQGEFLSVGTVVAVSAMLLLSGK 60

Query: 60  ----AMPGAPGWVILLLATIIACV-VAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSIL 114
               A+      V  ++A ++ C+ V   L  ++   A RP      LA +++ +G  I+
Sbjct: 61  DIHGALTPEDVTVWRMIAALVICMAVLGALGVLLYYTAVRPFVGGGGLAWVMSTLGFGII 120

Query: 115 LQTLAMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLG 174
           +Q  A+ +W P     P++L S    IGGA + P +IL+L  +   +  L  ++  T +G
Sbjct: 121 IQNAALAVWGPAAMVVPSILGSDVIRIGGAGVLPQEILVLVFSICIMLGLDLVMRKTKIG 180

Query: 175 RAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLK 234
           +A+RA A +   A+LMG+    V+   F+I + LA +AG++ A    TA   MG L  LK
Sbjct: 181 KAVRAVAHSKNAATLMGINVGAVVVLAFVISSGLAGVAGLLIAP-ITTASVFMGLLIALK 239

Query: 235 AFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILT 294
           AF+AA+ GG+ N  G ++GG +LG++EA+          GL  +   +I  F+++II+L 
Sbjct: 240 AFSAAIVGGLSNARGCMLGGFMLGIMEAM---------VGLWQAEMREISIFLLIIIVLV 290

Query: 295 LRPSGLLGERVADR 308
           ++P GLLG RV ++
Sbjct: 291 VKPEGLLGTRVVEK 304


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: 224
Number of extensions: 14
Number of successful extensions: 4
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: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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 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