Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate Pf6N2E2_1647 Maltose/maltodextrin ABC transporter, permease protein MalF
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1647 Length = 321 Score = 151 bits (381), Expect = 2e-41 Identities = 87/293 (29%), Positives = 158/293 (53%), Gaps = 19/293 (6%) Query: 31 AYAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAPFIGLKNYYEILFDEKS- 89 A+ L P +C+ + P+L+ + SL D + + +A F+GL NY LF + Sbjct: 30 AWLFLSPMLLCLALVAAWPLLRTFWFSLTDAS---LADTGDATFVGLSNY---LFHSSAG 83 Query: 90 ----LIRRGFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVP 145 L+ +W A+RNT +TVV LG+++A+L+N +F GR +VR +L+PW +P Sbjct: 84 WSGILVDPQWWNAVRNTLHFTVVSVGLEIVLGLMVALLLNVKFTGRALVRALILIPWAIP 143 Query: 146 SYVVGMTWGFLWRQDSGLINIILCDILHILPEKPYWLVGSN-QIWAIIIPTIWRGLPLSM 204 + V W ++ G+IN ++ L ++ W ++ +WA+II +W+ +P Sbjct: 144 TIVSAKIWSWMLNDQFGIINHLMLG-LGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVT 202 Query: 205 ILMLAGLQSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVS 264 +LMLA LQ + D YEAA +DG + + FW +TLPLL P L + +F ++ ++ F+++ Sbjct: 203 LLMLAALQMLPSDCYEAARVDGIHPVKVFWWVTLPLLMPALLVAAIFRILDSLRVFDVIY 262 Query: 265 MMFGNGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVALWY 317 ++ N + + Y +++ + G G+AA ++F V+ ++A+ Y Sbjct: 263 VLTSNSSSTMS-----MSVYARQHLVEFQDVGYGSAA-STLLFLVVAVIAMAY 309 Lambda K H 0.330 0.145 0.468 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: 345 Number of extensions: 25 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: 327 Length of database: 321 Length adjustment: 28 Effective length of query: 299 Effective length of database: 293 Effective search space: 87607 Effective search space used: 87607 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