GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Dinoroseobacter shibae DFL-12

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Dino:3607842
          Length = 351

 Score =  343 bits (879), Expect = 5e-99
 Identities = 186/336 (55%), Positives = 228/336 (67%), Gaps = 25/336 (7%)

Query: 17  VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76
           +  + L+   K +G  +V+ G+DL + DGEF +FVGPSGCGKSTLLR IAGLE+ + GS+
Sbjct: 1   MSGITLRGAVKRYGETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGSI 60

Query: 77  QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136
            I   +V  + P++RG+AMVFQ+YALYPH+TV +NMG GLK  GVPKAEI+ KVA A+ +
Sbjct: 61  HIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASEI 120

Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196
           L L+ YLAR+P  LSGGQRQRVAIGRAIVR P++FLFDEPLSNLDA LRV  R+EIARLH
Sbjct: 121 LKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180

Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256
           + + ATMIYVTHDQVEAMTLADKIVVL AGR+EQVG+P+ELY  P N+FVAGFIGSP MN
Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAMN 240

Query: 257 FIEA------------------AKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLG 298
           F++                      G     T+G+RP+HI L  E G     V   E LG
Sbjct: 241 FLDGRIENDAVHLAGLPPLPVPGAAGRSGPVTVGVRPQHIAL--EPGGDGYLVELTESLG 298

Query: 299 ADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPV 334
             + +Y+       LTV    E     D I   TPV
Sbjct: 299 GVSYLYLRGADGSRLTVEAGEE-----DPIAEGTPV 329


Lambda     K      H
   0.320    0.137    0.393 

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: 387
Number of extensions: 14
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: 352
Length of database: 351
Length adjustment: 29
Effective length of query: 323
Effective length of database: 322
Effective search space:   104006
Effective search space used:   104006
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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