Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate 17811 b3751 D-ribose transporter subunit (NCBI)
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__Keio:17811 Length = 296 Score = 122 bits (306), Expect = 1e-32 Identities = 93/305 (30%), Positives = 155/305 (50%), Gaps = 15/305 (4%) Query: 2 IKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPD 61 +K + + L A + AMA D ++ + V L NPFFV++ GA+ A K+ + Sbjct: 3 MKKLATLVSAVALSATVSANAMAKD----TIALVVSTLNNPFFVSLKDGAQKEADKLGYN 58 Query: 62 AKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVA 121 + V+ S+ + ++ +++ ++++N DS VG AVK A +A I V+ +D Sbjct: 59 --LVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQ 116 Query: 122 AAGADVT--VMSDNTMAGAESCKFLAEKLQGKGNVVIVNG-PPVSAVMDRVTGCKAEFKK 178 A +V + SDN + G + ++A+K V+ + G SA +R G + + Sbjct: 117 ATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQ-QAVA 175 Query: 179 SPGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDI 238 + +L+ +Q A R G+ M NLL A P + AVFA ND A+GA A++ A +SD+ Sbjct: 176 AHKFNVLA-SQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDV 234 Query: 239 KWISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPV 298 + G DG PD E+A+ D K AA+ AQ P + A+ V V+ G Q K + + Sbjct: 235 -MVVGFDGTPDGEKAVNDGK--LAATIAQLPDQIGAKGVETADKVLKGEKVQAKYP-VDL 290 Query: 299 KLITR 303 KL+ + Sbjct: 291 KLVVK 295 Lambda K H 0.314 0.129 0.360 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: 229 Number of extensions: 13 Number of successful extensions: 3 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: 316 Length of database: 296 Length adjustment: 27 Effective length of query: 289 Effective length of database: 269 Effective search space: 77741 Effective search space used: 77741 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: 48 (23.1 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