Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate BPHYT_RS16095 BPHYT_RS16095 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__BFirm:BPHYT_RS16095 Length = 369 Score = 355 bits (912), Expect = e-103 Identities = 196/362 (54%), Positives = 239/362 (66%), Gaps = 31/362 (8%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 + S+ L+ IRKA+ +EV++ I+LD+ DGEFV+FVGPSGCGKSTL+R IAGLED + G + Sbjct: 1 MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 IDG+ V VAPAKRGIAMVFQSYALYPH+T+ DNM GLK AG K EI+ V AA + Sbjct: 61 TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L ++ L R+P +LSGGQRQRVAIGRAI R+PK+FLFDEPLSNLDAALRV RLE ARLH Sbjct: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 LK TMIYVTHDQVEAMTLADKIVVL+AG +EQVGSP LY+ PAN FVAGFIGSP+MN Sbjct: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240 Query: 257 F--------------------------IEAAKLGDGEAKTIGIRPEHIGLSRESGDWKGK 290 F +E A + G+ T+GIRPEH+ + + Sbjct: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISAR 300 Query: 291 VIHVEHLGADTIIYIESETV--GLLT-VRLFGEHRYATDDIVHATPVIGSMHRFDADGRV 347 + VE LG +Y ES GL+ + H + ATP H FD+ G+ Sbjct: 301 TMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATP--EHCHLFDSAGKA 358 Query: 348 IK 349 + Sbjct: 359 FQ 360 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: 397 Number of extensions: 17 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: 352 Length of database: 369 Length adjustment: 29 Effective length of query: 323 Effective length of database: 340 Effective search space: 109820 Effective search space used: 109820 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