GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Caulobacter crescentus NA1000

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  212 bits (540), Expect = 1e-59
 Identities = 120/285 (42%), Positives = 168/285 (58%), Gaps = 18/285 (6%)

Query: 4   LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63
           + +R + K FG +  +  V +EI  GE +  +GPSG GK+TLLR IAGLE   +G + FD
Sbjct: 3   IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62

Query: 64  GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQL-AGKD---KQQCRKRVEAAAE 119
           GQ V   + + R +  VFQ YAL+ HMTV +N+AFG+ +  GKD   K +  +RVE   +
Sbjct: 63  GQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLK 122

Query: 120 MLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKL 179
           +++L     R P QLSGGQRQRVA+ RA+   P V L DEP   LDA +R + R E+ ++
Sbjct: 123 LVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRV 182

Query: 180 HRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPK 239
           H +   TT I+VTHDQ EA+ LADR+ +L +G +EQIGTP ++++ P + FV GF+G   
Sbjct: 183 HDATGVTT-IFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGEAN 241

Query: 240 M--------NFLSGAFAEPYK-----ADTIGIRAEHLEIDEQGGE 271
                     F +GA   P       A T  +R     +DE G E
Sbjct: 242 RFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGFE 286


Lambda     K      H
   0.321    0.138    0.396 

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: 327
Number of extensions: 15
Number of successful extensions: 3
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: 342
Length of database: 339
Length adjustment: 28
Effective length of query: 314
Effective length of database: 311
Effective search space:    97654
Effective search space used:    97654
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 (21.9 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