Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate WP_086510781.1 BZY95_RS15410 carbohydrate ABC transporter substrate-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >NCBI__GCF_002151265.1:WP_086510781.1 Length = 422 Score = 446 bits (1146), Expect = e-130 Identities = 225/430 (52%), Positives = 301/430 (70%), Gaps = 14/430 (3%) Query: 2 NAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTW 61 N + A ++ A+ ++L S+ AAE VEV+HWWTSGGE A +VLK +E +G+ W Sbjct: 6 NPFRKTALALATAAAASLTFSIQAAE----VEVLHWWTSGGEARAANVLKELMEAEGYGW 61 Query: 62 KDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENW 121 +D AVAGGGG TAMTVLKSRA++GNPP AQIKGP+IQEWG GLL L +V++AE W Sbjct: 62 EDFAVAGGGGETAMTVLKSRAMSGNPPSAAQIKGPEIQEWGELGLLGE--LDEVAEAEGW 119 Query: 122 DGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKL 181 D LL V+D +++ G YVAVPVN+HRVNWLW NP+V AG+E PTTL+E +AAG+ + Sbjct: 120 DELLPPTVADVMRHNGSYVAVPVNVHRVNWLWANPQVLAAAGVEM-PTTLDELFAAGEAI 178 Query: 182 KAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKK 241 + AG+I LAHGGQ WQD+TVFE V+L+ G + Y++ALV+LD + L M ++ K+ Sbjct: 179 REAGYIPLAHGGQAWQDATVFESVLLASGGTEFYQQALVELDPEALGSERMIEALETFKR 238 Query: 242 ITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEK 301 + MD + +GRDWNIA + VI G AGMQ+MGDWAK E+TAA AG++Y C A PGT+ Sbjct: 239 LRELMDADMSGRDWNIATSMVIEGSAGMQLMGDWAKGEFTAAGLTAGEEYLCAAAPGTQD 298 Query: 302 AFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDK 361 AFT+NIDS+A+F+++ + + AQQ LA++ L FQ+ F++ KGSIP R D +D Sbjct: 299 AFTFNIDSLAMFRVEGEER---EAQQALARLVLEPTFQEAFNLAKGSIPARPD----LDM 351 Query: 362 LGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKAS 421 GFD CAQ+S DF + GGL PSMAH MA VQGAIFDVVTN+ N +D +A+ Sbjct: 352 SGFDVCAQQSMDDFQRTAEEGGLVPSMAHGMAVRADVQGAIFDVVTNYFNSRDMAAEEAA 411 Query: 422 AQLASAVKAA 431 ++ +A +AA Sbjct: 412 RRMVNAAQAA 421 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: 516 Number of extensions: 17 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 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