GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM 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)



>lcl|FitnessBrowser__Cup4G11:RR42_RS01640 RR42_RS01640 ABC
           transporter permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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