Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 325 bits (834), Expect = 1e-93 Identities = 179/375 (47%), Positives = 247/375 (65%), Gaps = 12/375 (3%) Query: 1 MANLKIKNLQKGFEGFSI--IKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58 MA+L+++N+QK + I +K I L+++ EF++ VGPSGCGKSTL+ IAGLE ++GG Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAA 118 I +DG DI++ SP RD+AMVFQ+YALYP MSVR N++F L + V A++E++V+ A Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178 ++L++ P+LERKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238 +H+ L+ T +YVTHDQ+EAMT+ DKV V+ G I+Q G+P ++Y+ PANLFVA F+G+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 239 MGFLKGKITRVDSQ--GCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPG-- 294 M F+ +I + D + G + LP+ + LGIRPE + LA G Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGSA 300 Query: 295 DCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDA 354 D +L V +V E G DT V T + R+ D A R GETL+L D + LFDA Sbjct: 301 DFSLAVDIEVVEPTGPDTLV-VFTLNQVKACCRLAPDQAPRVGETLNLQFDPRRALLFDA 359 Query: 355 D-----GVALTRPLR 364 GV P+R Sbjct: 360 QTGERLGVVQPEPVR 374 Lambda K H 0.320 0.137 0.389 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: 380 Number of extensions: 12 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: 367 Length of database: 390 Length adjustment: 30 Effective length of query: 337 Effective length of database: 360 Effective search space: 121320 Effective search space used: 121320 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: 50 (23.9 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