Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate GFF3014 HP15_2958 extracellular solute-binding protein family 1
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__Marino:GFF3014 Length = 416 Score = 434 bits (1115), Expect = e-126 Identities = 223/421 (52%), Positives = 283/421 (67%), Gaps = 15/421 (3%) Query: 11 ISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGG 70 ++ A++SA L A ++ G VEV+HWWT+GGE A LK +E G TWKD AVAGGG Sbjct: 10 LTAAAVSAALLPAQALQA-GEVEVLHWWTAGGEARAAVALKEMMEDQGHTWKDFAVAGGG 68 Query: 71 GSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVS 130 G AMTVLK+RAV+GNPP AQIKG DI+EW G L++ L DV++A NW L+ ++ Sbjct: 69 GEAAMTVLKTRAVSGNPPAAAQIKGLDIREWAKLGFLTS--LDDVAEANNWGQLIPPVIA 126 Query: 131 DTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALA 190 D ++YE YVAVPVN+HRVNWLW NPE K G+ P TL+EFY A +KLKAAG LA Sbjct: 127 DVMQYEDSYVAVPVNVHRVNWLWANPETLNKVGVG-VPKTLDEFYQAAEKLKAAGITPLA 185 Query: 191 HGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNR 250 HGGQPWQD+TVFE V L+VMG D + A V+ D ++ +M + FAE K+ Y+D N Sbjct: 186 HGGQPWQDATVFEAVALAVMGPDDFASAFVEHDMDVINSAQMEEVFAEFAKVMSYVDDNA 245 Query: 251 AGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSM 310 AGRDWN A VI G+A MQ+MGDWAK E+TAA G+DY C A PGT FT+N+DS Sbjct: 246 AGRDWNTATGMVIRGEAAMQIMGDWAKGEFTAAGLTPGEDYVCAAAPGTGGQFTFNVDSF 305 Query: 311 AVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQK 370 A+F L + + AQ+DLA+ + +FQ VF+ KGSIPVR D FD CAQ Sbjct: 306 AMFSLSDE--DNTKAQKDLARTIMEPEFQAVFNKAKGSIPVRTD---------FDTCAQA 354 Query: 371 SAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVKA 430 S F + + GGL PS AH +AT+ VQG IFDVVTNF+N + DPA+A+ QLA+A++A Sbjct: 355 SMDTFKSSAEDGGLVPSFAHGLATTSYVQGQIFDVVTNFVNSDNKDPARATDQLAAAIQA 414 Query: 431 A 431 A Sbjct: 415 A 415 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: 541 Number of extensions: 24 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: 416 Length adjustment: 32 Effective length of query: 400 Effective length of database: 384 Effective search space: 153600 Effective search space used: 153600 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