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.
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:
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