GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pontibacter ramchanderi LP43

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_101443649.1 BD749_RS06040 ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>NCBI__GCF_002846395.1:WP_101443649.1
          Length = 317

 Score =  125 bits (313), Expect = 2e-33
 Identities = 92/302 (30%), Positives = 149/302 (49%), Gaps = 26/302 (8%)

Query: 18  VIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIV----NQLTPS 73
           V+ G+S      E +   G +G GKSTLL+ IAGL + ++G + F+G+ V    ++L P 
Sbjct: 8   VLHGISFRQGEYEKLAIAGETGSGKSTLLQAIAGLVQPSAGQITFEGKRVIGPHDKLVPG 67

Query: 74  RRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPRQ 133
             GIA + Q Y L   + V + + +   L G +        E   E+ +++   +R   Q
Sbjct: 68  HEGIAYLSQHYDLPQFLRVEQVLRYANILQGDE-------AETLYEVCRISHLKQRKTHQ 120

Query: 134 LSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHKTTMIYVTH 193
           LSGG+RQR+A+ R +   P + L DEP SNLD   +   +  I  +   +   T I ++H
Sbjct: 121 LSGGERQRIALARLLSTWPSLLLLDEPYSNLDKGHKELLKEVIHDITERL-AITCILISH 179

Query: 194 DQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFLSGAFAEPYKA 253
           D  + ++ ADRI +++ G + Q GTP ++Y  P   + AG  G+   N +    A P+ A
Sbjct: 180 DPHDTLSWADRILIIKGGRMVQQGTPEQVYRHPVDAYTAGLFGN--YNLIPAHVALPF-A 236

Query: 254 DTIGI---------RAEHLE-IDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIVRES 303
           + +GI         R EH   + ++ G  +GTV      G    + + + TG  V VR  
Sbjct: 237 EKLGIAVTARDLLVRPEHFRFVAKEAGSLNGTVQKVTFFGGYYDVQVQV-TGFSVTVRTQ 295

Query: 304 GI 305
            I
Sbjct: 296 AI 297


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: 257
Number of extensions: 18
Number of successful extensions: 4
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: 317
Length adjustment: 28
Effective length of query: 314
Effective length of database: 289
Effective search space:    90746
Effective search space used:    90746
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.

Links

Downloads

Related tools

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