Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 328 bits (842), Expect = 1e-94 Identities = 178/358 (49%), Positives = 231/358 (64%), Gaps = 34/358 (9%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 + S+Q++ I+K FGS +V++G+D+D+ DG+F + VGPSGCGKSTLLR IAGLE+ T+G + Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 I V + P +R IAMVFQ+YALYPH+TV DNM LK A K EI+ KVAKA+ + Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L L+ L R P +LSGGQRQRVA+GRAIVR+P++FLFDEPLSNLDA LRV R EI LH Sbjct: 121 LGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 + L+ T +YVTHDQ+EAMT+AD+IVV+ GR+EQ G P+ LY+ P NLFVAGFIGSP MN Sbjct: 181 QRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMN 240 Query: 257 FI---------------------------EAAKLGDGEAKTIGIRPEHIGLSRESGDWKG 289 F+ +A DG+ G+RPEH+ L + Sbjct: 241 FVPGVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTLGMPGQGLQT 300 Query: 290 KVIHVEHLGADTIIY---IESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDAD 344 +V VE GA+T IY E+E + + R H +A DI++ P H FDAD Sbjct: 301 RVSVVEPTGANTEIYSRFCEAEFISIFRER----HDFAAGDILNLVPDHQHTHLFDAD 354 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: 348 Number of extensions: 16 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: 359 Length adjustment: 29 Effective length of query: 323 Effective length of database: 330 Effective search space: 106590 Effective search space used: 106590 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