Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS04180 BPHYT_RS04180 sugar ABC transporter substrate-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__BFirm:BPHYT_RS04180 Length = 415 Score = 374 bits (959), Expect = e-108 Identities = 204/423 (48%), Positives = 263/423 (62%), Gaps = 15/423 (3%) Query: 9 TVISLASL-SALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVA 67 T++S A + S L S A + S+ V+HWWTSGGE A+ VLK ++K G+ WKD AVA Sbjct: 4 TLMSAAIVASTLATSAQVASAAESLSVLHWWTSGGESKAIRVLKDDMDKQGYEWKDFAVA 63 Query: 68 GGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSK-AENWDGLLS 126 GG G+ AMT LK++ ++GN P AQIKGP IQ+W G+L D+ K A +W L Sbjct: 64 GGAGAAAMTALKTQVMSGNAPSAAQIKGPLIQDWADQGVLV-----DIDKSATDWKAQLP 118 Query: 127 KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGF 186 +++ T+ +G YVA P ++HR+NWLWIN K G K PTT EF+A DK +AAG Sbjct: 119 AQINKTMMSKGHYVAAPFSVHRINWLWINKAALDKVG-GKPPTTWPEFFALADKFRAAGI 177 Query: 187 IALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYM 246 +A GGQPWQD T++E VVLS GAD Y+KA++DLDQKTL+ P+M + F +KI GY Sbjct: 178 TPVARGGQPWQDMTIWETVVLS-QGADFYRKAMIDLDQKTLTSPQMLQVFQTARKIQGYF 236 Query: 247 DPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYN 306 D GRDWN+A A VI+G GMQ MGDWAK E+ A K A DY C A PGT AFTY Sbjct: 237 DKGSTGRDWNLATAMVINGSGGMQFMGDWAKGEFANANKKADVDYICAAAPGTSNAFTYT 296 Query: 307 IDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDE 366 +DS F+ ++ + Q LAK + FQ+ FS+ KGSIPVR D+ MDK FD Sbjct: 297 VDSFVFFQQNGKKEATL-GQLALAKTIMSPAFQEQFSLYKGSIPVRQDV--SMDK--FDA 351 Query: 367 CAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLAS 426 CA+KS D K+ PS A S A +GAI DVVT FMN + DP +A ++A+ Sbjct: 352 CAKKSYADEQTTIKSNTFFPSFAFGDVQSSATEGAITDVVTGFMNSNE-DPQEAMRKVAA 410 Query: 427 AVK 429 A K Sbjct: 411 AAK 413 Lambda K H 0.314 0.129 0.377 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: 527 Number of extensions: 25 Number of successful extensions: 6 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: 432 Length of database: 415 Length adjustment: 32 Effective length of query: 400 Effective length of database: 383 Effective search space: 153200 Effective search space used: 153200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 51 (24.3 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