Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_01454 H281DRAFT_01454 carbohydrate ABC transporter substrate-binding protein, CUT1 family
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__Burk376:H281DRAFT_01454 Length = 412 Score = 248 bits (632), Expect = 3e-70 Identities = 160/419 (38%), Positives = 215/419 (51%), Gaps = 18/419 (4%) Query: 14 ASLSALPL-SVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGGS 72 A ++AL + VLA V+HWWTSGGE AA+ K G W D AVAG + Sbjct: 10 AMVAALAMHGVLAYAEPLKANVIHWWTSGGESAAIRQFADAYNKAGGQWIDNAVAGADQA 69 Query: 73 TAMTVLKSRAVAGNPPGVAQIK-GPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVSD 131 + + +R V G+PP AQ + GLL+ + DV+ ENW G+ + + D Sbjct: 70 RSTAI--NRIVGGDPPTAAQFNTSKQFHDLIDQGLLNN--VDDVAAKENWSGVFPQSILD 125 Query: 132 TVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALAH 191 ++K +G Y A PV+IH W + + F+KAGI P + +EF A KL+AAG I LA Sbjct: 126 SIKVKGHYYAAPVDIHMPAWFFYSKPAFQKAGITAEPQSYDEFIADLGKLRAAGVIPLAF 185 Query: 192 GGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNRA 251 GGQPWQ+ F+ V+ V G D Y K D D + K K++ ++D Sbjct: 186 GGQPWQEKITFDAVLADVGGPDLYLKVYRDHDANAVKSDAFKKVLIAFKRLHDFVDAGSP 245 Query: 252 GRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSMA 311 GR+WN A A VISGKAG+Q+MGDWAK E++AAK+ AGK++ C FPG Y + Sbjct: 246 GRNWNDATALVISGKAGVQIMGDWAKGEFSAAKQSAGKEFGC--FPGFGPHSPYLVAGDV 303 Query: 312 VFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQKS 371 K+D + AQ LA V Q FS KGSIP+R D +D D CA++ Sbjct: 304 FVFPKSDNASTVKAQNLLATVMTSPPAQVAFSAKKGSIPIRPD----VDAGSLDICAKEG 359 Query: 372 AKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVKA 430 I DK+ L M S QGA+ DVVTNF N K+ A A A+K+ Sbjct: 360 IA--IMKDKSRQLPNP---EMLLSPDTQGALIDVVTNFWN-KNQSVDDAQKAFAGALKS 412 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: 476 Number of extensions: 22 Number of successful extensions: 4 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: 412 Length adjustment: 32 Effective length of query: 400 Effective length of database: 380 Effective search space: 152000 Effective search space used: 152000 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: 50 (23.9 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