Align MalF, component of Maltose/trehalose porter (characterized)
to candidate PP_2262 PP_2262 sugar ABC transporter, permease protein
Query= TCDB::O51924 (300 letters) >FitnessBrowser__Putida:PP_2262 Length = 288 Score = 130 bits (327), Expect = 4e-35 Identities = 86/262 (32%), Positives = 139/262 (53%), Gaps = 3/262 (1%) Query: 25 MILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSAREFWYSTFVTV 84 ++LP+ +V ++P+M S+ +D+ + FVG Y +VL + Sbjct: 13 LVLPVFLLVAFSAVVPMMTVVNYSV-QDIFDQSSRYFVGADWYRQVLRDPALHDALLRQF 71 Query: 85 SFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELMYNYSYGL 144 +S + +E LG+ AL + + + V ++ IP +P + W++ GL Sbjct: 72 IYSACVLLIEIPLGIGIALAMPTKGRMASVCLIVMAIPLLIPWNVVGTIWQIFGRADIGL 131 Query: 145 FNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLYEAALID 204 L+ LGVS N+ G P A+ +++ DVW T L+ LL +GL+AIP Y+AA ID Sbjct: 132 LGASLAKLGVS-YNYAGDPFDAWLTVLVMDVWHWTSLVALLCYSGLRAIPDVYYQAARID 190 Query: 205 GASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSIS-LLAFN 263 AS + F+ I LP LK VL++AL+LR +D+ ++ +VLTGGGPG ATT +S L Sbjct: 191 RASGWAVFRHIQLPKLKNVLVIALMLRFMDSFMIYTEPFVLTGGGPGNATTFLSQTLTRM 250 Query: 264 YYNLGDYGIGSAISILTFVLVL 285 D G +A S++ F+++L Sbjct: 251 AVGQFDLGPAAAFSLVYFLIIL 272 Lambda K H 0.329 0.145 0.436 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: 257 Number of extensions: 20 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: 300 Length of database: 288 Length adjustment: 26 Effective length of query: 274 Effective length of database: 262 Effective search space: 71788 Effective search space used: 71788 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