Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 210 bits (534), Expect = 6e-59 Identities = 141/378 (37%), Positives = 204/378 (53%), Gaps = 32/378 (8%) Query: 1 MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTI 60 MA + + + K + +++ G+ L VN E +GPSGCGK+ LLRLIAG E AGTI Sbjct: 1 MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60 Query: 61 ELDGRDITE------VSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKV 114 + G +++ V P RDL +VFQ YA++PHMSV N+ + L LAG+ AE ++V Sbjct: 61 SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120 Query: 115 NEAARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRL 174 E ++ L + R P QLSGGQ+QRVA+ RA+V P + L DEPL NLDA LR +MR Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180 Query: 175 ELARLHKELQATMIYVTHDQVEAMTLADKVVVL-NGGRIEQVGSPLELYHQPANLFVAGF 233 E+ L + L T++YVTHDQ A+ ++D++ ++ + G I QVG+P E++ +PA+ FV F Sbjct: 181 EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF 240 Query: 234 LGTPKMGFLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAV--TLGIRPEHLNLA 291 +G FL R+ +L AG +P L G A G RP + LA Sbjct: 241 MGV--ANFLPA------RRRGMAMLAAGGEQPVPW---GLPDGDAEHWMAGFRPSDVRLA 289 Query: 292 LPGDCTLQVTADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHC-- 349 GD L+ T + LG+ T +++ G + ++ A G + + E C Sbjct: 290 RQGD-GLRGTVRRASFLGAMT-DYLIEVDGASFRTQLDTHEALARG---LMFAEGEPCVV 344 Query: 350 -----HLFDANGVAVARP 362 H FDA VA P Sbjct: 345 GFHDLHWFDAATVAAQAP 362 Lambda K H 0.321 0.137 0.390 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: 332 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: 367 Length of database: 366 Length adjustment: 30 Effective length of query: 337 Effective length of database: 336 Effective search space: 113232 Effective search space used: 113232 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