Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 316 bits (809), Expect = 7e-91 Identities = 166/307 (54%), Positives = 215/307 (70%), Gaps = 15/307 (4%) Query: 17 VGSLQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75 + S+QL ++K + G+ E +KGIDL++ DGEFV+ VGPSGCGKSTLLR +AGLE T G+ Sbjct: 1 MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60 Query: 76 VQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAG 135 ++ID V + PA+R IAMVFQ+YALYPH+TV N+ GLK GV + EIE +V AA Sbjct: 61 LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120 Query: 136 MLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARL 195 ML +EP+L R+P +LSGGQRQRVA+GRA+VREP FLFDEPLSNLDA LRV R+EI +L Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180 Query: 196 HRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQM 255 R LK T +YVTHDQ+EA+TL D++VVLN G IEQVG+PME+Y +PA++FVA FIGSP M Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240 Query: 256 NFIEAAKLGD-----------GEAKTIGIRPEHIGLSRESGDW---KGKVIHVEHLGADT 301 N + A L + + IGIRP+ + + D G V E GA++ Sbjct: 241 NMLPVAYLRERGANGLLDHLAADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAES 300 Query: 302 IIYIESE 308 +Y+ E Sbjct: 301 HLYVSLE 307 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: 351 Number of extensions: 14 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: 352 Length of database: 354 Length adjustment: 29 Effective length of query: 323 Effective length of database: 325 Effective search space: 104975 Effective search space used: 104975 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.
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