Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00415 BPHYT_RS00415 sugar ABC transporter substrate-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__BFirm:BPHYT_RS00415 Length = 422 Score = 403 bits (1035), Expect = e-117 Identities = 207/420 (49%), Positives = 269/420 (64%), Gaps = 11/420 (2%) Query: 11 ISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGG 70 +++ +L + A VEV+H+WTSGGE + VLK +++ G TWKD AVAGGG Sbjct: 11 LTVYALGVAAVLACGAARSAEVEVLHYWTSGGEAKSAQVLKQMLDEKGDTWKDFAVAGGG 70 Query: 71 GSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVS 130 G AMT LK+R +AGNPP AQIKGP IQEWG G+L + + DV+K E WD L+ ++S Sbjct: 71 GGNAMTALKTRVIAGNPPAAAQIKGPAIQEWGDEGVLVS--INDVAKREGWDKLIPPQIS 128 Query: 131 DTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALA 190 +KY+G YVA PVN+HRVN LWIN + KK + P T +EF+ + L+ AG +A Sbjct: 129 GIMKYKGQYVAAPVNVHRVNRLWINADALKKVNAQP-PATWDEFFRTAEALQKAGITPVA 187 Query: 191 HGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNR 250 GGQ WQD+ FE V L V GA Y+KA V LDQ TL GP M K+ KKI Y D + Sbjct: 188 IGGQQWQDAETFETVALGVGGAAFYEKAFVQLDQSTLRGPTMVKALETFKKIKAYTDKAQ 247 Query: 251 AGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSM 310 GRDWN+A VISGKA MQ MGDWAK E++ A K+ GKDY CV PG++ A+T+N+DS Sbjct: 248 TGRDWNLATGMVISGKAAMQFMGDWAKGEFSVAGKVPGKDYLCVPAPGSQNAYTFNVDSF 307 Query: 311 AVFKLKADRKGDI-AAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQ 369 A FK+ R D+ Q+DLA + L FQ++F++NKGSIPVR MD FD CAQ Sbjct: 308 AFFKV---RSADVEKGQKDLASLLLSPKFQEIFNLNKGSIPVRQG----MDLSKFDTCAQ 360 Query: 370 KSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVK 429 +SA DF + G L PS AH+M + AV+GA +DV+ NF ND + +A+ +LA A K Sbjct: 361 RSAADFTSAQAKGTLVPSWAHDMVDTPAVEGAFYDVIGNFWNDDNESAQQAADKLAVAAK 420 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: 565 Number of extensions: 28 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: 432 Length of database: 422 Length adjustment: 32 Effective length of query: 400 Effective length of database: 390 Effective search space: 156000 Effective search space used: 156000 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