GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuK in Phaeobacter inhibens BS107

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate GFF2754 PGA1_c27970 ATP-binding transport protein SmoK

Query= TCDB::Q9R9Q4
         (342 letters)



>lcl|FitnessBrowser__Phaeo:GFF2754 PGA1_c27970 ATP-binding transport
           protein SmoK
          Length = 331

 Score =  333 bits (854), Expect = 4e-96
 Identities = 176/333 (52%), Positives = 229/333 (68%), Gaps = 2/333 (0%)

Query: 1   MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60
           M  LQL ++ KSFG  +V+K +++ ++ GEF+VFVGPSGCGKSTLLR+I+GLE+ T+G +
Sbjct: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60

Query: 61  AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120
           +  GQ V    P++RGIAMVFQSYALYPH++V ENMA  ++   + K++   RV  A+ M
Sbjct: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120

Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180
           L L  YL+R P +LSGGQRQRVAIGRA+VR+PK+FLFDEPLSNLDAALR+ TRLEIA+LH
Sbjct: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180

Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240
           R +   +MIYVTHDQ+EAMTLAD+I VLRDG +EQ+GTP+ELY  P + FVA FIG+P M
Sbjct: 181 RQL-SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAM 239

Query: 241 NFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIV 300
           NF+            IGIR E+  I    G  +G VIH E LG D+ I +D+G       
Sbjct: 240 NFVPAQRLGGNPGQFIGIRPEYARISPV-GPLAGEVIHVEKLGGDTNILVDMGEDLTFTA 298

Query: 301 RESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333
           R  G      G+T++          FD  G+ +
Sbjct: 299 RLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI 331


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: 371
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: 331
Length adjustment: 28
Effective length of query: 314
Effective length of database: 303
Effective search space:    95142
Effective search space used:    95142
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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