Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein
Query= uniprot:A0A165KPY4 (416 letters) >lcl|FitnessBrowser__Phaeo:GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein Length = 409 Score = 235 bits (600), Expect = 2e-66 Identities = 141/411 (34%), Positives = 219/411 (53%), Gaps = 13/411 (3%) Query: 3 KMTKIAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKG-HTWRDFAVAG 61 K+T I +A A + ++EV H+WTSGGEA +V + + G+ H W D A+AG Sbjct: 2 KLTSILMTTALSVSATIAQSADLEVTHWWTSGGEAAAVTKFADAVNGQTTHNWVDGAIAG 61 Query: 62 GGGDSAMTVLKSRVISGNPPSAAQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELL-PKV 119 G +A ++ SR++ G+P +A Q T G +E G++ ++ LA+ E W +++ P Sbjct: 62 SG-TTARPIIISRILGGDPMAATQLTHGRQAEELIEAGLMTDLTELAEQEGWRDIVNPPS 120 Query: 120 VADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVP 179 + D Y+G PVN+H W+W S EA KAG++ +P+ W EF AAA KL AG+VP Sbjct: 121 LLDSCTYEGRIYCVPVNIHSTQWLWLSHEAFDKAGMS-VPQDWYEFVAAAPKLAEAGIVP 179 Query: 180 VAHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDP 239 +A G Q WQ F ++ +G+ ++ ++ D K + + Sbjct: 180 LAMGQQGWQQRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDARELAR- 238 Query: 240 GAPGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVD 299 + +DWNLAT M+I GKAG Q+MGDWA+GEF A + G+D+ C G + D Sbjct: 239 NSNVQDWNLATNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQIIDTSGD 298 Query: 300 SFILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKD 359 +F + DA ++AQ D+AS ++S Q FNL KGS+PVR + +DC K Sbjct: 299 AFYFPVIDDAEVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGDVDLSAANDCMKKGLAI 358 Query: 360 FVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIA 410 D G ++PS A + T+ I+D++++FW D ++ ADA + A Sbjct: 359 LAD----GNVLPSM--DQAFSADTQAQIQDLMAEFWASD-MAAADAQARYA 402 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: 469 Number of extensions: 22 Number of successful extensions: 7 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: 409 Length adjustment: 31 Effective length of query: 385 Effective length of database: 378 Effective search space: 145530 Effective search space used: 145530 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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