Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease
Query= SwissProt::O51924 (295 letters) >NCBI__GCF_000018545.1:WP_015888140.1 Length = 307 Score = 213 bits (542), Expect = 4e-60 Identities = 111/281 (39%), Positives = 179/281 (63%), Gaps = 4/281 (1%) Query: 11 YREAKLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKP--FVGLRNYLRVLSA 68 + E L YLM+ P + ++L I P + F+ ++HR ++ P+ P FVG+ N+ R+LS Sbjct: 22 WAERHLRYLMLAPTVLILLALTIFPSIYMFYAAVHR-ISPNPDLPWEFVGVGNFARLLSD 80 Query: 69 REFWYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISART 128 +F + TV F+ V+V+LE +LGL AL+L+ ++ L+ +++IP +P I A T Sbjct: 81 PQFHVALRNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAIT 140 Query: 129 WELMYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAI 188 W+L+Y +G+ N I+ +LG+ W G A F+I++ADVW+ TPF+ LL+LAGL ++ Sbjct: 141 WKLIYEPQFGVLNEIMFLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASL 200 Query: 189 PQDLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGA 248 P + YEAA +DGAS + +F +TLP LKPV+ +AL+LR +DALR+FD++++LTGGGP Sbjct: 201 PVEPYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADR 260 Query: 249 TTSISLLAFNY-YNLGDYGIGSAISILTFVLVLSFTIVYLK 288 T +SL + Y D G +AIS+ + + + ++K Sbjct: 261 TKVLSLYIYQVAYRFADPGYAAAISLFVLFVTIVLSTWFMK 301 Lambda K H 0.329 0.145 0.439 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: 275 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: 295 Length of database: 307 Length adjustment: 27 Effective length of query: 268 Effective length of database: 280 Effective search space: 75040 Effective search space used: 75040 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 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