Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate 17640 b3579 predicted transporter (NCBI)
Query= reanno::psRCH2:GFF2082 (338 letters) >FitnessBrowser__Keio:17640 Length = 328 Score = 208 bits (530), Expect = 1e-58 Identities = 112/315 (35%), Positives = 184/315 (58%), Gaps = 13/315 (4%) Query: 23 AQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKASGGKLKVRTFASASLGSDDQMQ 82 A + + + +RFGY ++ +Q AAK + + + + G+LK++ F ++LG+ M Sbjct: 17 AFSTSSLAAQSLRFGYETSQTDSQHIAAKKFNDLLQERTKGELKLKLFPDSTLGNAQAMI 76 Query: 83 NALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQADQVLDGPVGRQVMDKLEEKG 142 + + GG +M + + G+S M + D PFLF D A + LDG VG + LE KG Sbjct: 77 SGVRGGTIDMEMSGSNNFAGLSPVMNLLDVPFLFRDTAHAHKTLDGKVGDDLKASLEGKG 136 Query: 143 LVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNPVFIDTFKRMGANAVPLPFSELF 202 L L YWENG+R+VTNS P++ D G+K+R +P+ I FK GAN +P+PF+E++ Sbjct: 137 LKVLAYWENGWRDVTNSRAPVKTPADLKGLKIRTNNSPMNIAAFKVFGANPIPMPFAEVY 196 Query: 203 TALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYSPWIVTVSKRWWDGLSATEQGIL 262 T LET+ +D QE+P N + S+KF+EVQK+LS+T+H YSP +V ++K +DGLS Q L Sbjct: 197 TGLETRTIDAQEHPINVVWSAKFFEVQKFLSLTHHAYSPLLVVINKAKFDGLSPEFQQAL 256 Query: 263 MEAAEKARDAEREDTRREASQALAALKERGMQINEVSPDEIQRMREKAQPAIQTVIDAVG 322 + +A++A + +R+ + + + +KE G+++ I + KA DA+G Sbjct: 257 VSSAQEAGNYQRKLVAEDQQKIIDGMKEAGVEV-------ITDLDRKA------FSDALG 303 Query: 323 QELFDQVQAEVEKAA 337 ++ D +V + A Sbjct: 304 NQVRDMFVKDVPQGA 318 Lambda K H 0.315 0.131 0.368 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: 236 Number of extensions: 8 Number of successful extensions: 1 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: 338 Length of database: 328 Length adjustment: 28 Effective length of query: 310 Effective length of database: 300 Effective search space: 93000 Effective search space used: 93000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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