GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Methanobacterium lacus AL-21

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_013645165.1 METBO_RS07885 ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>NCBI__GCF_000191585.1:WP_013645165.1
          Length = 230

 Score =  123 bits (308), Expect = 5e-33
 Identities = 82/210 (39%), Positives = 118/210 (56%), Gaps = 18/210 (8%)

Query: 17  DVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIVNQLTPSR-- 74
           + ++G+++ +  GEF+  +GPSG GKSTL+ LI  L+  T G L  DG+ ++ +  S   
Sbjct: 22  NALRGLNITVDEGEFVSIMGPSGSGKSTLMNLIGCLDTPTEGELTIDGREISSMKESELT 81

Query: 75  ----RGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQ----QCRKRVEAAAEMLQLTPY 126
                 I  +FQ++ L P ++V +N+ F M+    DK+      R R E   E + L   
Sbjct: 82  KVRAEKIGFIFQTFNLLPALSVRDNVEFPMRNLSGDKKLNKSARRARAEECLECVGLGHR 141

Query: 127 LERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHK- 185
           L+ LP +LSGG+RQRVAI RA+V  PK  L DEP  NLD      +   I KL   ++  
Sbjct: 142 LDHLPAKLSGGERQRVAIARALVNKPKFILADEPTGNLD----TESTENIMKLLHDINDM 197

Query: 186 -TTMIYVTHDQVEAMTLADRICVLRDGLVE 214
            TT+I VTHD VE  T   RI  +RDG++E
Sbjct: 198 GTTVIMVTHD-VET-TENTRILRIRDGVIE 225



 Score = 23.1 bits (48), Expect = 0.007
 Identities = 12/40 (30%), Positives = 17/40 (42%)

Query: 256 IGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTG 295
           +G R +HL     GGE     I   ++    +I  D  TG
Sbjct: 138 LGHRLDHLPAKLSGGERQRVAIARALVNKPKFILADEPTG 177


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: 160
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 342
Length of database: 230
Length adjustment: 26
Effective length of query: 316
Effective length of database: 204
Effective search space:    64464
Effective search space used:    64464
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 Apr 09 2024. 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