Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 223 bits (569), Expect = 5e-63 Identities = 145/345 (42%), Positives = 206/345 (59%), Gaps = 21/345 (6%) Query: 18 IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDI------TEVS 71 I+KG+ L+VN E V +GPSG GK+TLLR IAGLE S G+I + + + EVS Sbjct: 20 ILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKKIEVS 79 Query: 72 PAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKP 131 KR L VFQ+YAL+PH +V +N+++ L L V E+ ++V E L LG + ER P Sbjct: 80 VEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLSERHP 139 Query: 132 KQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQATMIYVT 191 QLSGGQ+QRVA+ R++V NP++ L DEPLSNLDA LR + R+ L +L +L + + VT Sbjct: 140 HQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSAVCVT 199 Query: 192 HDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLKGKITRVDS 251 HDQ EAM MADKVV+L G IEQ G+P ++Y P +LFVA F+G + G +T VD Sbjct: 200 HDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGANNT--ISGLVTDVDG 257 Query: 252 QGCEVQLDAGTRVSLPLGGR---HLSVGSAVTLGIRPEHLELAK-PGDCALQVTADVSER 307 ++ + L GR L G T +R E ++LA+ P + +L++ S Sbjct: 258 DSARIEGNGWA-----LRGRLRTPLKAGDRATAVVRLEKIKLAQTPKENSLRLPLTASVY 312 Query: 308 LGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLF 352 LG +T+ +V +G T+R G+ + GE L + + A+H LF Sbjct: 313 LG-NTWEYVFDLAG--ATIRGYGNEFMQPGEQL-VDIPAEHLWLF 353 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: 310 Number of extensions: 12 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: 353 Length adjustment: 29 Effective length of query: 338 Effective length of database: 324 Effective search space: 109512 Effective search space used: 109512 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 Apr 09 2024. 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