Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate GFF1857 Psest_1896 ABC-type sugar transport system, periplasmic component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__psRCH2:GFF1857 Length = 415 Score = 513 bits (1322), Expect = e-150 Identities = 264/432 (61%), Positives = 316/432 (73%), Gaps = 17/432 (3%) Query: 1 MNAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFT 60 MNA RLA +SLA L VLA G VEV+HWWTSGGEK A D L+ VE+ G + Sbjct: 1 MNAFHRLALSVSLA------LPVLA--HAGEVEVLHWWTSGGEKRAADTLQKLVEQKGHS 52 Query: 61 WKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAEN 120 WKD AVAGGGG AMTVLK+RAV+GNPP AQIKGPDIQEWG GLL+ L D +KAE Sbjct: 53 WKDFAVAGGGGEAAMTVLKTRAVSGNPPSAAQIKGPDIQEWGELGLLAN--LDDTAKAER 110 Query: 121 WDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDK 180 WD LL ++V ++Y+G YVAVPVN+HRVNWLWINPEVF+KAG K P TL+EF+AA DK Sbjct: 111 WDALLPEQVRKIMQYDGSYVAVPVNVHRVNWLWINPEVFEKAGA-KPPKTLDEFFAAADK 169 Query: 181 LKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELK 240 LKAAGFI +AHGGQPWQD TVFE VLS++G D Y KA V+LD TL+G +M ++F LK Sbjct: 170 LKAAGFIPVAHGGQPWQDGTVFEGFVLSILGPDDYHKAFVELDNDTLTGDKMVQAFTALK 229 Query: 241 KITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTE 300 K+ Y+D + AGR+WN A VI GKAGMQ+MGDWAKSE+TAA K+AGK+YQC+ FPGT+ Sbjct: 230 KLRDYIDADAAGREWNRATGMVIDGKAGMQIMGDWAKSEFTAANKVAGKNYQCLPFPGTQ 289 Query: 301 KAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMD 360 +F +NIDS+A+FKL +D + AQ+DLA+ L +FQ F+ NKGSIPVR D D Sbjct: 290 GSFAFNIDSLAMFKLSSD--DNRKAQEDLARTVLEPEFQTFFNQNKGSIPVRQD----QD 343 Query: 361 KLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKA 420 FD CAQ+S DF K GLQPS+ H MA S VQGA+FDVVTNF ND ADP KA Sbjct: 344 MSEFDACAQQSMTDFKEAAKGSGLQPSLTHGMAASSYVQGAVFDVVTNFFNDPKADPQKA 403 Query: 421 SAQLASAVKAAQ 432 + QLA+A+KA Q Sbjct: 404 AKQLAAAIKAVQ 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: 583 Number of extensions: 26 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: 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