GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691
          Length = 351

 Score =  234 bits (597), Expect = 3e-66
 Identities = 120/238 (50%), Positives = 165/238 (69%), Gaps = 2/238 (0%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           M  L L NV K YG+     +K++ L + EG+ +  +GPSGCGK+TL+  IAGLET+TGG
Sbjct: 1   MTGLILENVEKHYGSAC--AVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I +  +D+       R+  MVFQS AL+P M+V ENI + LK+R + +AD  A V  + 
Sbjct: 59  EIRLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELL 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           +L+Q++ +++R   +LSGGQ+QRVA+ RA+A RPKI L DEPLS LDAKLR  M+ E++ 
Sbjct: 119 ELIQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQ 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGS 238
           + QRL  TT+ VTHDQ EAMT+ D V V+ +  +QQ G+P EIY +PAN+FVA FIGS
Sbjct: 179 LQQRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGS 236


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: 330
Number of extensions: 9
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: 351
Length adjustment: 30
Effective length of query: 356
Effective length of database: 321
Effective search space:   114276
Effective search space used:   114276
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: 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 (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