Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate WP_090447189.1 BLS63_RS18140 carbohydrate ABC transporter substrate-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >NCBI__GCF_900100495.1:WP_090447189.1 Length = 417 Score = 538 bits (1386), Expect = e-157 Identities = 275/433 (63%), Positives = 331/433 (76%), Gaps = 17/433 (3%) Query: 1 MNAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFT 60 MNAISRLAT +SLASL +PLS LA G VEV+HWWTSGGEK AVD L+ VE G + Sbjct: 1 MNAISRLATAVSLASL--MPLSALA----GEVEVLHWWTSGGEKRAVDTLQKLVEDQGHS 54 Query: 61 WKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAEN 120 WKD AVAGGGG AMTVLK+RAV+GNPP AQIKGPDIQEWG GLL+ L V++ + Sbjct: 55 WKDFAVAGGGGEAAMTVLKTRAVSGNPPAAAQIKGPDIQEWGELGLLAD--LDQVAEEQQ 112 Query: 121 WDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDK 180 WD LL ++V + +++ GDYVAVPVN+HRVNWLWINPEVF KAG PTTL+EF+AA DK Sbjct: 113 WDKLLPEQVVEVMQFGGDYVAVPVNVHRVNWLWINPEVFAKAGATP-PTTLDEFFAAADK 171 Query: 181 LKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELK 240 LKAAGFI LAHGGQPWQDSTVFED+ L ++G + KA V+LD+ L+GP+M + FA L+ Sbjct: 172 LKAAGFIPLAHGGQPWQDSTVFEDLALGLLGPQDFHKAFVELDKDILTGPKMVEVFAALQ 231 Query: 241 KITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTE 300 K+ GY+D N AGRDWN A A V++GKAGMQ+MGDWAKSEWTAA K+AG DYQC+ FPGT+ Sbjct: 232 KLHGYVDANAAGRDWNSATAMVMNGKAGMQIMGDWAKSEWTAAGKVAGSDYQCLPFPGTQ 291 Query: 301 KAFTYNIDSMAVFKLK-ADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEM 359 +F +NIDS+A+FKL AD + AQ+DLA+ +GT+FQ+VF+ NKGSIPVR D Sbjct: 292 GSFAFNIDSLAMFKLSDADNR---KAQEDLARTVMGTEFQRVFNQNKGSIPVRLD----Q 344 Query: 360 DKLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAK 419 D FD CAQ+S DF A GGLQPS+AH MA S VQGA+FDVVTNF ND ADP K Sbjct: 345 DMSVFDACAQQSMADFKAAAANGGLQPSLAHGMAASSYVQGAVFDVVTNFFNDPKADPQK 404 Query: 420 ASAQLASAVKAAQ 432 A+ QLA+A++A Q Sbjct: 405 AAQQLAAAIQAVQ 417 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: 603 Number of extensions: 23 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: 417 Length adjustment: 32 Effective length of query: 400 Effective length of database: 385 Effective search space: 154000 Effective search space used: 154000 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 24 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