Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate AO353_03395 AO353_03395 sugar ABC transporter substrate-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03395 Length = 435 Score = 799 bits (2064), Expect = 0.0 Identities = 398/435 (91%), Positives = 414/435 (95%), Gaps = 3/435 (0%) Query: 1 MNAISRLATVISLASL---SALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 57 MNAISRLATV+SLA+L +A PLS LAA+SKGSVEVVHWWTSGGEKAAVDVLKAQVEKD Sbjct: 1 MNAISRLATVVSLATLFPLTAFPLSALAADSKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 60 Query: 58 GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSK 117 GFTWKDGAVAGGGG+TAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALK VSK Sbjct: 61 GFTWKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKGVSK 120 Query: 118 AENWDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAA 177 AENWDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINP VFKKAGI+KAPTTLEEFYAA Sbjct: 121 AENWDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPAVFKKAGIDKAPTTLEEFYAA 180 Query: 178 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFA 237 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMG +GYKKALVDLDQKTLSGPEM KSF Sbjct: 181 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGPEGYKKALVDLDQKTLSGPEMVKSFT 240 Query: 238 ELKKITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFP 297 ELKK+TGYMDPNRAGRDWNIAAADVI+GKAGMQMMGDWAKSEWTAA K+AGKDYQCV FP Sbjct: 241 ELKKLTGYMDPNRAGRDWNIAAADVINGKAGMQMMGDWAKSEWTAAHKVAGKDYQCVPFP 300 Query: 298 GTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLN 357 GTEKAFTYNIDS+AVFKLKADR GDIAAQQDLAKVALG DFQKVFS+NKGSIPVR DMLN Sbjct: 301 GTEKAFTYNIDSLAVFKLKADRTGDIAAQQDLAKVALGKDFQKVFSINKGSIPVRTDMLN 360 Query: 358 EMDKLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADP 417 +M GFD CAQ SAKDF+AD+KTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDK ADP Sbjct: 361 DMSAAGFDSCAQASAKDFLADEKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKSADP 420 Query: 418 AKASAQLASAVKAAQ 432 AKASAQLASA+KAAQ Sbjct: 421 AKASAQLASAIKAAQ 435 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: 785 Number of extensions: 19 Number of successful extensions: 2 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: 435 Length adjustment: 32 Effective length of query: 400 Effective length of database: 403 Effective search space: 161200 Effective search space used: 161200 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