Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 341 bits (875), Expect = 2e-98 Identities = 190/371 (51%), Positives = 249/371 (67%), Gaps = 16/371 (4%) Query: 1 MSALEIRNIRKRYGEV--ETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 MS LE+R+IRK Y V ETLKGIDI + SGEFL+L+G SGCGKSTL+N IAGL + G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 59 DILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118 I++ + + + PKDRDIAMVFQSYALYP +SV NI FGL++R +P+ E D+ V A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 LLQI L+++KP+ LSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K+ Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 LHQ L+TT+VYVTHDQIEAMTLA RIAV++DG ++QL P EVYDRP L+VAGF+GSP Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 239 MNI--LDAEMTANGLKIE-----GCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGS 291 M+ + E GL+ E G LP+P A G++V +GIRPE + Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFL--ADRVGKKVILGIRPEHITQPQDQ 298 Query: 292 E-AQRLTA----SVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTAL 346 + Q L A ++EV E TGP+++ + + + P V G FD + Sbjct: 299 KNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKV 358 Query: 347 HLFDPESGRSL 357 FDPE+ + + Sbjct: 359 VFFDPETEKRI 369 Lambda K H 0.320 0.136 0.385 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: 379 Number of extensions: 13 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: 360 Length of database: 372 Length adjustment: 30 Effective length of query: 330 Effective length of database: 342 Effective search space: 112860 Effective search space used: 112860 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