Align ABC transporter permease (characterized, see rationale)
to candidate GFF2751 PGA1_c27940 ABC transporter permease protein
Query= uniprot:A0A165KPZ4 (293 letters) >FitnessBrowser__Phaeo:GFF2751 Length = 308 Score = 109 bits (272), Expect = 9e-29 Identities = 89/288 (30%), Positives = 134/288 (46%), Gaps = 15/288 (5%) Query: 9 WLPKLVVAPAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRW---- 64 W + +APA VL + I ++N + S ++ GLA +E L+ W Sbjct: 12 WHIAVFLAPA-VLVYTAIMIFPLFNTLRLALYSESDQIRQFVGLANFETLFGNPNWSEQF 70 Query: 65 WVALKNLGIFGVGYVGGSLLIGVVLAVLLDQ-KIRAEGALRTIYLYPMALSFVVTGTAWK 123 W AL N F ++ IGV LA +L ++R RT P LSFV+ G AWK Sbjct: 71 WNALGNNFWFFFVHMLVQNPIGVALAAILSHPRLRFAALYRTAIFVPTILSFVIVGFAWK 130 Query: 124 WLLNPGLGIEKMVRDWGFPNFEFG-WLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGI 182 +L+P GI + D + F WL + A+ + + +WQ G M L A L I Sbjct: 131 LILSPIWGITPDLLDAIGLKWLFAPWLGKEDYALTTLALISVWQFVGIPMMLIYAALLSI 190 Query: 183 DDSIIKAAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLA-IKSFDLVMAL--TAGGP 239 + +I+A +VDG + +W+I LP + P + +L+ + +FDL+ GP Sbjct: 191 PEEVIEAGEVDGITGMSAFWKIKLPLILP-SIGIISILTFVGNFNAFDLIYTTQGALAGP 249 Query: 240 GFATDVPATFMYTMSF----SRGQIGLGAASATMMLATVAALVIPYLY 283 F+TD+ TFMY F G +G+A AT M A + V YL+ Sbjct: 250 DFSTDILGTFMYRTFFGFQLQLGDPHMGSAIATAMFAIILIGVCIYLF 297 Lambda K H 0.327 0.141 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: 303 Number of extensions: 16 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: 293 Length of database: 308 Length adjustment: 27 Effective length of query: 266 Effective length of database: 281 Effective search space: 74746 Effective search space used: 74746 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: 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