GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Cupriavidus basilensis 4G11

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate RR42_RS29445 RR42_RS29445 ABC transporter permease

Query= uniprot:A0A159ZYE0
         (418 letters)



>FitnessBrowser__Cup4G11:RR42_RS29445
          Length = 358

 Score =  158 bits (400), Expect = 2e-43
 Identities = 103/320 (32%), Positives = 166/320 (51%), Gaps = 35/320 (10%)

Query: 98  LIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYAL 157
           L+   L+ P + S   +     +LIY + GLGL ++ G  GLL +G+  F  VGAY+ A 
Sbjct: 28  LMACLLIAPGWASSYWIAQLGFVLIYAIAGLGLMVLSGYTGLLSIGHAAFLGVGAYTQAW 87

Query: 158 LSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDI 217
           L+ + G+ F   L  A  ++A  G ++G P LR++G YLAI TL FG I+   L     +
Sbjct: 88  LTSH-GVPFVPALLAAAALSALTGVVVGLPALRVKGIYLAIATLAFGLIVEEILARWESV 146

Query: 218 TGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAAL 277
           TGG  G+  +  P  +G   +                       V F YL   +  LA L
Sbjct: 147 TGGNAGLP-VAAPQLWGYVLD---------------------GPVAFYYLSLAVCLLATL 184

Query: 278 FVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGL 337
            V+N LLR   GRA+ A+R+ EI+ +++G++    K  +F L AA  G AG+ +A +   
Sbjct: 185 AVLN-LLRSATGRAFIAIRDSEISAQSMGIHLARYKTLSFALSAALVGIAGALYAHKLRY 243

Query: 338 VTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEM-----------MREFSEY 386
           ++PE F   +S  +L +VV+GG+GS  G  L AI +I++P+M           + + S  
Sbjct: 244 ISPEQFGIAQSIDLLLLVVVGGLGSVHGAFLGAIFLIVMPQMIVLAKDLLPPAIGQASGM 303

Query: 387 RMLMFGALMVLMMIWRPQGL 406
           + L++G +++  +++ P GL
Sbjct: 304 QALVYGLVLMAFVLFEPMGL 323


Lambda     K      H
   0.331    0.145    0.439 

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: 424
Number of extensions: 25
Number of successful extensions: 5
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: 418
Length of database: 358
Length adjustment: 30
Effective length of query: 388
Effective length of database: 328
Effective search space:   127264
Effective search space used:   127264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 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