Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease
Query= TCDB::Q72H67 (291 letters) >FitnessBrowser__Koxy:BWI76_RS23380 Length = 296 Score = 143 bits (360), Expect = 5e-39 Identities = 86/285 (30%), Positives = 156/285 (54%), Gaps = 14/285 (4%) Query: 5 RQVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLF-QDP 63 + + LAWI P ++ +++ +P F+ SF + D+ + PP F G+ENY Y+ +D Sbjct: 5 KMLGLAWIS--PYIIGLIVFTAFPFVSSFFLSFTEYDL--MSPPVFNGIENYRYMLTEDG 60 Query: 64 DFRQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVS-AKM 122 F +++ T + +++ L+ L IA +++ RG G RTA IP + + V+ A + Sbjct: 61 LFWKSMGVTFAYVFLTIPLKLAFALGIAFVLNFKLRGIGFFRTAYYIPSILGSSVAIAVL 120 Query: 123 WQWMLNDVYGVINVLGVKLGLLS-QKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGL 181 W+ + + + +L +G+L V +L P L L S+ + VW+ M ++ LA L Sbjct: 121 WRAL----FAIDGLLNSFIGVLGFDPVNWLGEPSLALMSVTLLRVWQFGSAM-VIFLAAL 175 Query: 182 QMIPEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP 241 Q +P+ YEAA IDGAS+WQ F +T+PL+TP + I +T A + F +V++G P Sbjct: 176 QNVPQSQYEAAMIDGASKWQMFMKVTVPLITPVIFFNFIMQTTQAFQEFTGPYVITGGGP 235 Query: 242 --ATRTLAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRT 284 +T ++Y T + D+GYG+A++ + +++ F + ++ Sbjct: 236 TYSTYLFSLYIYDTAFKYFDMGYGAALAWVLFLVVAVFAAIAFKS 280 Lambda K H 0.329 0.142 0.433 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: 256 Number of extensions: 20 Number of successful extensions: 5 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: 291 Length of database: 296 Length adjustment: 26 Effective length of query: 265 Effective length of database: 270 Effective search space: 71550 Effective search space used: 71550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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