GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Croceitalea dokdonensis DOKDO 023

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_054557498.1 I595_RS00860 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_001306415.1:WP_054557498.1
          Length = 219

 Score =  127 bits (319), Expect = 3e-34
 Identities = 71/215 (33%), Positives = 118/215 (54%), Gaps = 10/215 (4%)

Query: 8   NIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSG---GDILIGE 64
           NI+K YG+++ LKG+ I+++ GE + ++G SG GK+TLL ++  L  PS      I+I  
Sbjct: 6   NIKKNYGDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPKDSSIMING 65

Query: 65  RSVLGVHPK------DRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118
             V  +  K      + +I  +FQ + L P  +   N+     +++ P+A+ +   R+  
Sbjct: 66  VDVTDLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCIPAFIKKTPKAKAEVRGRELL 125

Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178
             L +    D +P +LSGG++QRVA+ RAL+ NP V   DEP  NLD++    +     +
Sbjct: 126 DFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSESAENLHQLFFK 185

Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIE 213
           L +    T V VTH++ E   +A R  +M DG+I+
Sbjct: 186 LREEFGQTFVIVTHNK-ELANMADRKLIMVDGQIQ 219


Lambda     K      H
   0.320    0.136    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: 168
Number of extensions: 7
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: 360
Length of database: 219
Length adjustment: 26
Effective length of query: 334
Effective length of database: 193
Effective search space:    64462
Effective search space used:    64462
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 (21.8 bits)
S2: 47 (22.7 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