Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate WP_086510782.1 BZY95_RS15415 sugar ABC transporter permease
Query= SwissProt::O51924 (295 letters) >NCBI__GCF_002151265.1:WP_086510782.1 Length = 310 Score = 137 bits (346), Expect = 2e-37 Identities = 86/277 (31%), Positives = 150/277 (54%), Gaps = 3/277 (1%) Query: 13 EAKLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSAREFW 72 +A L L++ P + L F+ ++ TF +SL +P FVG Y R+++ +W Sbjct: 25 QAWLPKLVLAPSAAISLFFVYGFMLWTFVLSLTNS-RMLPSYEFVGFAQYARLMANDRWW 83 Query: 73 YSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELM 132 ++ V F + V++ LGL A++L++R++ G LR I L P A+ I++ W+ + Sbjct: 84 VASTNLVVFGGLFVAICLALGLVLAILLDQRIRQEGALRTIYLYPMALSFIVTGVVWKWL 143 Query: 133 YNYSYGLFNWILSI-LGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAIPQD 191 N G+ + S +WL P A + +VIA VW+ + F+ L LAGL+ I Sbjct: 144 LNPGLGIQAMVRSWGFENFRFDWLVDPDMAVYTLVIAAVWQASGFVMALFLAGLRGIDDS 203 Query: 192 LYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTS 251 + +AA +DGAS+ + + +P L+PV+ A+++ + A++ FD++ LTGGGPG A+ Sbjct: 204 ILKAAQLDGASLPRIYWRVVIPCLRPVVFSAVMILSHIAIKSFDLVVALTGGGPGYASDL 263 Query: 252 ISLLAFNY-YNLGDYGIGSAISILTFVLVLSFTIVYL 287 + + + + G+GSA ++L VL+ I YL Sbjct: 264 PATFMYAHAFTRAQIGLGSASAMLMLGGVLAILIPYL 300 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: 222 Number of extensions: 7 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: 310 Length adjustment: 27 Effective length of query: 268 Effective length of database: 283 Effective search space: 75844 Effective search space used: 75844 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