GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Pseudomonas simiae WCS417

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__WCS417:GFF4321
          Length = 386

 Score =  319 bits (818), Expect = 8e-92
 Identities = 176/381 (46%), Positives = 245/381 (64%), Gaps = 7/381 (1%)

Query: 1   MADIHCQALAKHYAGG-PPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59
           MA +  + + K Y  G P  L  ++L I +GEF++L+GPSGCGKST++  IAGLE I+GG
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 60  TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119
            + IG   V+ +  ++R++AMVFQ+YALYP MSV +NI FGL+  K P A+ID  V  VA
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120

Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179
            LL +E LL RKP  +SGGQQQR A+ RA+ + P ++LFDEPLSNLDAKLR ++R ++K 
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239
           +HQRL+TTTVYVTHDQ+EAMTL D+V +M+DG I Q G+P E+Y  P N F A FIG+P 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240

Query: 240 MNFLSGTVQRQDGQL--FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRI-AGEREP 296
           MNF+   +QR+DG+L   +++   R  L             V L +RP+ + + AGE + 
Sbjct: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300

Query: 297 AASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356
           A+S+     V++ E  G D L+  +  D  +   +  D  PQ G TLTL  D  ++ +FD
Sbjct: 301 ASSIR--AEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358

Query: 357 VESGENLSLPDAALTAPGSDD 377
             +GE L    ++L A G  D
Sbjct: 359 ANTGERLGTA-SSLPAQGHAD 378


Lambda     K      H
   0.321    0.137    0.403 

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: 379
Number of extensions: 13
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: 406
Length of database: 386
Length adjustment: 31
Effective length of query: 375
Effective length of database: 355
Effective search space:   133125
Effective search space used:   133125
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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