Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_041755751.1 PST_RS17365 maltose ABC transporter permease MalF
Query= uniprot:C8WUR0 (321 letters) >NCBI__GCF_000013785.1:WP_041755751.1 Length = 510 Score = 179 bits (455), Expect = 1e-49 Identities = 98/252 (38%), Positives = 149/252 (59%), Gaps = 7/252 (2%) Query: 64 FVGLKNYEELLNPHDPLSNLFLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTL 123 F G N+ +L+ + F+ F WT +A T VGL LA LL + +R + Sbjct: 256 FAGFANFTRVLS-EPSIREPFVQIFAWTFAFAGLTVVFTLAVGLVLASLLQWELVRGKAF 314 Query: 124 YRTLLIVPWAVPNLISMLAWQGLLNDQYGQINALLHGVFGLPRIPWLTSALWARIAVIMV 183 YR +LI+P+AVP IS+L ++GL N +G+IN LL G+FG+ R W + AR +++V Sbjct: 315 YRLMLILPYAVPGFISILVFRGLFNQNFGEINLLLEGLFGI-RPDWFSDPTLARTMILIV 373 Query: 184 NVWAGFPYMMTVCLGALQSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFS 243 N W G+PYM+ +C+G LQ+IP DQYEA+ IDGA+ +T+P + + +PLLI F+ Sbjct: 374 NTWLGYPYMLLLCMGLLQAIPRDQYEASAIDGASPLDNLLRITLPQLIKPLMPLLIACFA 433 Query: 244 YNFNNFNASYLLTGGGPP--NSNNPFLGQTDILATAAYKMTLTFNRYD--LGATISVLLF 299 +NFNNF LLT GGP + P G TD+L + Y++ + D L A I+ ++F Sbjct: 434 FNFNNFVLITLLTRGGPDIIGATTP-AGTTDLLVSYTYRIAFQDSGQDFALAAAIATMIF 492 Query: 300 ILVALISWVQMR 311 ILV ++ + ++ Sbjct: 493 ILVGAMALLNLK 504 Score = 32.7 bits (73), Expect = 2e-05 Identities = 14/38 (36%), Positives = 23/38 (60%) Query: 24 AYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLS 61 A Y+ P++ + V I P+ YT+ I FTN++ + LS Sbjct: 66 AQRYIFPSVAGMLVFVIFPLLYTVGIGFTNYSGSNLLS 103 Lambda K H 0.327 0.140 0.451 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: 431 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 321 Length of database: 510 Length adjustment: 31 Effective length of query: 290 Effective length of database: 479 Effective search space: 138910 Effective search space used: 138910 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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