GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Hydrogenovibrio kuenenii DSM 12350

Align TreV, component of Trehalose porter (characterized)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000526715.1:WP_024851725.1
          Length = 282

 Score =  144 bits (362), Expect = 3e-39
 Identities = 81/217 (37%), Positives = 131/217 (60%), Gaps = 12/217 (5%)

Query: 9   VKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITD 68
           + K G   V+  I   ++  EF  ++G SG GKSTLL+I+ G+EKL KG+++ D  +I +
Sbjct: 15  ITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVLVD-EEIVN 73

Query: 69  KPPEKRNVAMVFQNYALYPNMSVRDNIAFP--LKMRGMKKE-----EIIERVEKAAKLLG 121
           KP + R  AMVFQ+Y+LYP ++V++NI F   LK+ G          +++R      L+G
Sbjct: 74  KPGKDR--AMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRSYALLDLMG 131

Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181
           + ++ D    Q+SGG +QRVA+ARA++  P   L+DEP   LDA+ R      +  + + 
Sbjct: 132 LEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHDLILHLFEI 191

Query: 182 LKGTFIYVTHDQKEALSLADRIAIL--HKGKFEQVSD 216
            K T ++VTHD +EA+ LADR+ ++  + G+ + + D
Sbjct: 192 EKSTIVFVTHDVEEAIYLADRVVVMAPNPGRIDSIYD 228


Lambda     K      H
   0.318    0.137    0.385 

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: 231
Number of extensions: 10
Number of successful extensions: 3
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: 324
Length of database: 282
Length adjustment: 27
Effective length of query: 297
Effective length of database: 255
Effective search space:    75735
Effective search space used:    75735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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