Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF1918 PGA1_c19500 putative sugar-binding periplasmic protein
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__Phaeo:GFF1918 Length = 414 Score = 271 bits (693), Expect = 3e-77 Identities = 149/416 (35%), Positives = 231/416 (55%), Gaps = 14/416 (3%) Query: 2 WKMTKIAAVA-VGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVA 60 +K +A VA + + +A +A EV+H+W S GEA ++ G W D + Sbjct: 3 FKSNLLAGVATLAMTSAATADGIRAEVIHWWVSAGEAAAIKVFADAYTANGGEWIDNGIG 62 Query: 61 GGGGDSAMTVLKSRVISGNPPSAAQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELLPKV 119 GGG A T +R++ G+ P Q +E G+L ++D A+A W L P + Sbjct: 63 GGG---AKTTFVNRLMGGDAPQVGQFNTSREFEEIVDAGLLHSLDAEAEAGNWSALFPGI 119 Query: 120 VADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVP 179 + +V+K G+Y A PVN+H NW+W +++ + AG+ +P WD FF AA+ LK AG++P Sbjct: 120 IDNVVKRDGSYYAVPVNIHGSNWLWHNNQVMADAGLD-VPTDWDSFFEAAETLKEAGIIP 178 Query: 180 VAHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGY--- 236 +A GG+ WQ+ TF SV+L VGG Y + D TALTSD MK+ + + R++ Sbjct: 179 LAVGGEAWQERLTFNSVLLSVGGQDLYLRLFEEKDTTALTSDEMKEVFDVYSRLRTLVRE 238 Query: 237 TDPGAPGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTF 296 TDPG+PGR WN AT M+I G+A Q+MGDWAKGEFL+AG PG ++ C A + + + Sbjct: 239 TDPGSPGRSWNDATNMVITGQAAMQIMGDWAKGEFLSAGMTPGVEYGCTPAVIAGSPYMI 298 Query: 297 NVDSFILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKAS 356 + D F+ K + ++AQS +A++++ Q FN KGSIPVR + D C + + Sbjct: 299 SGDVFVFPKTGNEEDREAQSLMATTMLDAEVQVAFNNIKGSIPVRPDVDTSQLDVCGQQA 358 Query: 357 AKDFVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAA 412 + G+ M I+ GA++DV +QFWN + ++ +A+ ++ A Sbjct: 359 IALTSNPDTHVGVTQ-----MYISSDLAGALQDVYTQFWNSETMTTEEAITLLSQA 409 Lambda K H 0.315 0.128 0.383 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: 503 Number of extensions: 17 Number of successful extensions: 5 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: 416 Length of database: 414 Length adjustment: 31 Effective length of query: 385 Effective length of database: 383 Effective search space: 147455 Effective search space used: 147455 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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