GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Escherichia coli BW25113

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Keio:15248
          Length = 378

 Score =  234 bits (598), Expect = 2e-66
 Identities = 125/288 (43%), Positives = 187/288 (64%), Gaps = 6/288 (2%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           ++L  + K +     + +  ++L+I  GEFL L+GPSGCGK+T++  IAGLET+  G IM
Sbjct: 18  VQLAGIRKCFDG--KEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           + ++D++ +  ++R +  VFQSYAL+P M+V EN+ FGL+++K P A+I   V    +++
Sbjct: 76  LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMV 135

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           Q+E    RKP QLSGGQQQRVA+ RA+  +P++ L DE LS LD KLR +M+ E+K + +
Sbjct: 136 QLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQR 195

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
           +L  T V+VTHDQ EA+T+ D++ VM+DG I+Q GTP+EIY  P N FVA FIG   M F
Sbjct: 196 KLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM-F 254

Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQI 291
               ++R D + V     G+  C + +N      +   V+  LRPE +
Sbjct: 255 NATVIERLDEQRVRANVEGR-ECNIYVNFAVEPGQKLHVL--LRPEDL 299


Lambda     K      H
   0.318    0.135    0.382 

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: 326
Number of extensions: 13
Number of successful extensions: 1
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: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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