GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisQ in Herbaspirillum seropedicae SmR1

Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate HSERO_RS19340 HSERO_RS19340 amino acid ABC transporter permease

Query= uniprot:Q88GX3
         (239 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19340 HSERO_RS19340 amino acid
           ABC transporter permease
          Length = 216

 Score =  101 bits (251), Expect = 1e-26
 Identities = 68/213 (31%), Positives = 101/213 (47%), Gaps = 12/213 (5%)

Query: 19  LLAGALVTVSLALACLPIGLPLGLVVALAARSRKRLPRAWATTFSTVFRGLPELLTLLII 78
           LL  A+ TV L+L     G   G V+AL   S   + R  A+ +  V +G+P L+ L + 
Sbjct: 12  LLQAAVWTVVLSLVAFVFGGVAGFVIALWRVSPNAVLRGIASGYIQVVQGIPLLVILFVA 71

Query: 79  YYGCQIAAQKILAAMGYQGEFLINTFLAAMIAFSLVFAAFSSEIWLAAFKTLPKGQLEAC 138
           Y+G  IA             F +   +AA I+F++  AAF  EIW    + +PK Q EA 
Sbjct: 72  YFGLAIAG------------FKLTPLVAAGISFAIYCAAFLGEIWRGCIQAVPKTQWEAS 119

Query: 139 SALGLSKRTGFFKVLLPQLTRIALPGLSNNWLSLLKDTSLVSTISLVDLMRQTNLAVSVT 198
             LG ++     KV+LPQ  +IA P      + ++K+TSL S I  VDL R   +  + T
Sbjct: 120 ECLGFNRFEQLTKVILPQAVKIATPPTVGFMVQIVKNTSLASVIGFVDLSRAGQIINNST 179

Query: 199 KEPMFFYGVACLGYLLFAALSGRVFAYIERRSN 231
            +P   +G   L Y         +  + ER+ N
Sbjct: 180 FQPFTVFGCVALIYFCLCFPLSALSKHFERKLN 212


Lambda     K      H
   0.328    0.139    0.410 

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: 120
Number of extensions: 8
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: 239
Length of database: 216
Length adjustment: 22
Effective length of query: 217
Effective length of database: 194
Effective search space:    42098
Effective search space used:    42098
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 (21.8 bits)
S2: 46 (22.3 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