GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Cupriavidus basilensis 4G11

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS01640 RR42_RS01640 ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Cup4G11:RR42_RS01640
          Length = 358

 Score =  151 bits (381), Expect = 3e-41
 Identities = 113/340 (33%), Positives = 172/340 (50%), Gaps = 34/340 (10%)

Query: 9   IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68
           ++ AVA + +PL+   +  + + I    L++ L ALGLNI+ GYAG L LG  AF AVGA
Sbjct: 31  VLMAVAFVAIPLLGSEYWFSAILIP--FLIFALAALGLNILTGYAGQLSLGTAAFMAVGA 88

Query: 69  YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128
           Y          A NF     +   GL   L  ++  A L AA  G   G P+L+++G YL
Sbjct: 89  YA---------AYNFQ----LRIEGLPVLLTFIL--AGLSAAMVGVAFGLPSLRIKGFYL 133

Query: 129 AIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTL 188
           A+ TL     +   L       N ++              G+   ++L +FG  I++   
Sbjct: 134 AVATLAAQFFVVWALTKFPWFSNNSSS-------------GVITAQQLNLFGIAIDTPVK 180

Query: 189 YYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFG 248
            Y   L+LV V  I+   L  S  GRAWM++R+ ++AA+ +GI     KLLAF + + + 
Sbjct: 181 KYLFVLMLVTVLAIVAKNLVRSSTGRAWMSVRDMDVAAEVIGIPLMRTKLLAFAVSSFYC 240

Query: 249 GVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYV 307
           GV+GA++   + G V P+ FSL  S  ++ M+++GG+G I G  LGA  +  LP  L   
Sbjct: 241 GVAGALYAFCYLGSVEPDGFSLDLSFRVLFMIIIGGVGSILGSFLGAAFILLLPIFLDIA 300

Query: 308 AGPLQAMTDGRLDSAILR--QLLIALAMIIIML-LRPRGL 344
             PL A+      +A +   QL++   +II  L + P GL
Sbjct: 301 LPPLAALLHLPFTNAAVSHIQLMVFGGLIIFFLVVEPHGL 340


Lambda     K      H
   0.328    0.144    0.430 

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: 321
Number of extensions: 13
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: 358
Length of database: 358
Length adjustment: 29
Effective length of query: 329
Effective length of database: 329
Effective search space:   108241
Effective search space used:   108241
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: 49 (23.5 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