GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudovibrio axinellae Ad2

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_068006976.1 PsAD2_RS14030 ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>NCBI__GCF_001623255.1:WP_068006976.1
          Length = 361

 Score =  273 bits (699), Expect = 4e-78
 Identities = 155/356 (43%), Positives = 213/356 (59%), Gaps = 31/356 (8%)

Query: 1   MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60
           M  ++++D+   FG  +V+K +++ I  GEF+V +G SGCGKSTLL  +AGL +++ G +
Sbjct: 1   MNSIEIKDLSLRFGEVEVLKNLNLSIHKGEFLVLLGSSGCGKSTLLNCVAGLLDLSHGQI 60

Query: 61  AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120
             D + V    P  RGI MVFQSYALYP M+V  N++FG++ AG  K +  KR++ AAE+
Sbjct: 61  FIDERNVTWEEPKDRGIGMVFQSYALYPQMSVRGNLSFGLKNAGIPKAEIAKRIQRAAEI 120

Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180
           LQ+   L R P  LSGGQRQRVAIGRA+VRD  VFLFDEPLSNLDA LR   R+EI +LH
Sbjct: 121 LQIQDLLHRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVEINRLH 180

Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240
             + K TMIYVTHDQ+EAMTLADRI V+RDG + Q+  P ++Y  P + ++AGFIGSP M
Sbjct: 181 HRL-KNTMIYVTHDQIEAMTLADRIAVMRDGNILQLDVPSQIYNRPINKYIAGFIGSPSM 239

Query: 241 NFLSGAFA-------------------------EPYKADTIGIRAEHLEIDEQGGEW--S 273
           NFL G  +                         +   A T+G+R EH+       E   S
Sbjct: 240 NFLEGKLSAGDNPSFIFGDERFDMSRYRFDGEGQQNGATTLGVRPEHIRTGNAAQEMPIS 299

Query: 274 GTVIHS--EMLGSDSYIYLDIGTGEPVIVRESGIAKHQPGQTIRISPAAGQVHRFD 327
             ++    E +GSD+ +   +  G+   +R  G+A    G  + +     QV  F+
Sbjct: 300 RNIVVEVVEPMGSDTLVRTHL-AGQEFRLRMDGLASVNKGDNLLVGFDPAQVSLFE 354


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: 355
Number of extensions: 17
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: 361
Length adjustment: 29
Effective length of query: 313
Effective length of database: 332
Effective search space:   103916
Effective search space used:   103916
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