GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Methanospirillum stamsii Pt1

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_109940760.1 DLD82_RS08835 ATP-binding cassette domain-containing protein

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_003173335.1:WP_109940760.1
          Length = 348

 Score =  212 bits (540), Expect = 1e-59
 Identities = 105/262 (40%), Positives = 165/262 (62%), Gaps = 10/262 (3%)

Query: 19  LFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADRDLA 78
           L ++ LDI  GE++V +GP+G GK+ LL T+AG     SG+I + GRD+T + P DR++ 
Sbjct: 16  LRNVTLDITPGEYLVIIGPTGAGKTILLETIAGFYPPDSGKIIMDGRDITNIPPKDRNIC 75

Query: 79  MVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQ 138
           MV+Q Y L+PH+TV EN+ FG+K    +P+  +++  E AR+L ++  L RKP  LSGG+
Sbjct: 76  MVYQDYMLFPHLTVEENIGFGLKTRKKDPEYIRKKTVEMARLLSIDHLLHRKPETLSGGE 135

Query: 139 RQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAM 198
           +QR AI R++V  P++ L DEPLS LD + R ++R EL  +H     T++++TH+  E  
Sbjct: 136 QQRAAIARSLVMEPNLLLLDEPLSALDGQTRDKLRTELRRIHDITNVTVVHITHNFEEVF 195

Query: 199 TMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDVGLQD----ISLD 254
           ++AD++ ++N+G I Q+G+P +++ KP S F+A F G    N+F      QD    I +D
Sbjct: 196 SLADRVAIMNKGEIVQIGNPDEVFRKPESEFIASFTGME--NIFKGSCSHQDGISAIKID 253

Query: 255 A----SAAFVGCRPEHIEIVPD 272
                SA  +G R  +  I P+
Sbjct: 254 GHIVYSATCLGEREVYATIRPE 275


Lambda     K      H
   0.320    0.139    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: 292
Number of extensions: 11
Number of successful extensions: 1
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: 338
Length of database: 348
Length adjustment: 29
Effective length of query: 309
Effective length of database: 319
Effective search space:    98571
Effective search space used:    98571
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: 49 (23.5 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