Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 337 bits (864), Expect = 3e-97 Identities = 178/355 (50%), Positives = 230/355 (64%), Gaps = 29/355 (8%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 + S+Q++ ++K FGS ++++G+D+D+ DGEF + VGPSGCGKSTLLR +AGLE+ T G + Sbjct: 1 MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 I G V +V P R IAMVFQ+YALYPH+TV+DNM L A KA ++E+V KAA + Sbjct: 61 LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L L L R P +LSGGQRQRVA+GRAIVR+P++FLFDEPLSNLDA LRV R EI LH Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 + LK T IYVTHDQ+EAMT+AD+IVV+ G +EQ G P++LY+ PANLFVAGFIGSP MN Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240 Query: 257 FIEAA--------------------------KLGDGEAKTIGIRPEHIGLSRESGDWKGK 290 FI A + DG+ T G+RPEH+ + K Sbjct: 241 FIPATLRRNATGAEVEFADGTRVPAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQGIATK 300 Query: 291 VIHVEHLGADTIIYIESETVGLLTVRLFGE-HRYATDDIVHATPVIGSMHRFDAD 344 VI VE GADT ++ L ++ F E H + D++H P H FDA+ Sbjct: 301 VIVVEPTGADTEVFSRFGDTSLTSI--FRERHDFGAGDVIHLVPDHSRTHLFDAE 353 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: 360 Number of extensions: 18 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: 361 Length adjustment: 29 Effective length of query: 323 Effective length of database: 332 Effective search space: 107236 Effective search space used: 107236 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