GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Phyllobacterium brassicacearum STM 196

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_106712312.1 CU102_RS17070 ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>NCBI__GCF_003010955.1:WP_106712312.1
          Length = 332

 Score =  369 bits (948), Expect = e-107
 Identities = 185/333 (55%), Positives = 244/333 (73%), Gaps = 1/333 (0%)

Query: 1   MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60
           M  + L+ + KSFG   VI  + +EI  GEF+VFVGPSGCGKSTLLR+IAGLE+++ G +
Sbjct: 1   MGSITLQKVSKSFGTTSVIPEIDLEINDGEFVVFVGPSGCGKSTLLRMIAGLEDLSGGRI 60

Query: 61  AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120
             DG+ ++   P++RG++MVFQSYALYPHM+VY N+AF +++ G+DK    K+V+ AA +
Sbjct: 61  VIDGKDMSNEAPAKRGLSMVFQSYALYPHMSVYGNIAFPLKMDGQDKTAIDKKVKDAAHI 120

Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180
           L LT YL+R P QLSGGQRQRVAIGRAIVR PK FLFDEPLSNLDAALR   RLEI+ LH
Sbjct: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVRQPKAFLFDEPLSNLDAALRGNMRLEISDLH 180

Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240
             + KTTMIYVTHDQVEAMT+AD+I VL  G +EQ+G+PL+LY +P +VFVAGFIGSP+M
Sbjct: 181 HQL-KTTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLDLYRSPRNVFVAGFIGSPRM 239

Query: 241 NFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIV 300
           N + G  A    A T+G+R EH+ I +  G W G V  +E LGSD++I++ +     + V
Sbjct: 240 NLIEGQEAAKQSAVTLGVRPEHMRISKTEGTWKGIVGVTEHLGSDTFIHVQVDGVGKITV 299

Query: 301 RESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333
           R  G    + GQ + ++P   ++HRFDA G+A+
Sbjct: 300 RTDGDFSTEFGQQVYLTPEPARLHRFDADGQAI 332


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: 378
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: 342
Length of database: 332
Length adjustment: 28
Effective length of query: 314
Effective length of database: 304
Effective search space:    95456
Effective search space used:    95456
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 24 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