Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >MicrobesOnline__882:207786 Length = 397 Score = 168 bits (425), Expect = 3e-46 Identities = 109/319 (34%), Positives = 172/319 (53%), Gaps = 24/319 (7%) Query: 21 GID---LEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEVSP----- 72 G+D +V + E VV +G SG GKSTL+R + L E + GT+ +DGRD+T + Sbjct: 42 GVDRASFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRR 101 Query: 73 -AKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKP 131 +R MVFQ +AL+PH +V +N +F L+ GV +AE E++ + + L +P Sbjct: 102 LRQRSFGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRP 161 Query: 132 KQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQATMIYVT 191 QLSGG +QRV + RA+ +P I L DE S LD +R M+ ELLRL +LQ T+++++ Sbjct: 162 AQLSGGMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFIS 221 Query: 192 HDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLKGKITRVDS 251 HD EA+ + D++V++ G + Q+G+P D+ PA+ +VA F+G + +T+V + Sbjct: 222 HDLDEALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVG-------EADVTKVLT 274 Query: 252 QGCEVQLDAGTRVSLPLGG-----RHLSVGSAVTLGIRPEHLELAK--PGDCALQVTADV 304 G ++ V L + G R + + TL + E L D A ++ A+ Sbjct: 275 AGSVMKRSEAVAV-LGIDGPRTALRKMRRNAIATLFVLDERHRLVGLITADDAARLAAEG 333 Query: 305 SERLGSDTFCHVRTASGEA 323 LGS + T EA Sbjct: 334 VRELGSIVRRDIATVPPEA 352 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: 306 Number of extensions: 17 Number of successful extensions: 2 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: 397 Length adjustment: 30 Effective length of query: 337 Effective length of database: 367 Effective search space: 123679 Effective search space used: 123679 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