GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Pseudomonas fluorescens FW300-N2E2

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889
          Length = 386

 Score =  322 bits (826), Expect = 9e-93
 Identities = 174/368 (47%), Positives = 237/368 (64%), Gaps = 4/368 (1%)

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

Query: 60  TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119
            + IG   V+ +  ++R++AMVFQ+YALYP MSV +NI FGL+  K   A ID  V  VA
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQAAIDEEVTRVA 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 ++Y  P NLF A FIG+P 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240

Query: 240 MNFLSGTVQRQDGQL--FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPA 297
           MNF+   +QR+DG+L   +++   R  L             V L +RP+ + +AG  EP 
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQDAGLEDREVILGMRPEQIMLAGS-EPN 299

Query: 298 ASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDV 357
              T    V++ E  G D L+     D  +   +  D  PQPG TLTL  D  ++ +FD 
Sbjct: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPQPGETLTLQFDPSKVLLFDA 359

Query: 358 ESGENLSL 365
           +SGE L +
Sbjct: 360 QSGERLGV 367


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: 395
Number of extensions: 15
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.

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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