GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Sphingomonas koreensis DSMZ 15582

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__Korea:Ga0059261_3874
          Length = 243

 Score =  115 bits (288), Expect = 1e-30
 Identities = 77/224 (34%), Positives = 116/224 (51%), Gaps = 16/224 (7%)

Query: 2   AELQLRDIRKSFGAFDV----IKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITS 57
           A +  R++ KS+    V    + GVS+ + PGE  + VGPSGCGKSTLL +++GL     
Sbjct: 7   AAIDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQ 66

Query: 58  GTLAFDGQIVNQLTPSRR------GIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCR 111
           G +   G  + ++    R          VFQ + L+  +T  E +A+ +Q       + R
Sbjct: 67  GEVDALGNPICRMKAGARDAFRLANTGFVFQGFNLFNALTAEEQVAYVLQCMKVKPAEAR 126

Query: 112 KRVEAAAEMLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVA 171
           +R  AA E + L P +   P +LSGG++QRVAI RA+ + P++   DEP S LD+    A
Sbjct: 127 QRARAALEAVGLGPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHA 186

Query: 172 TRLEIAKLHRSMHK--TTMIYVTHDQVEAMTLADRICVLRDGLV 213
               IA L    H     ++ VTHD    ++ ADRI  + DG +
Sbjct: 187 V---IALLRDIAHNQGAAVLCVTHDP-RLLSFADRIIHMEDGRI 226


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: 198
Number of extensions: 11
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: 243
Length adjustment: 26
Effective length of query: 316
Effective length of database: 217
Effective search space:    68572
Effective search space used:    68572
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: 47 (22.7 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