Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate HSERO_RS05315 HSERO_RS05315 LacI family transcriptional regulator
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS05315 Length = 302 Score = 164 bits (414), Expect = 3e-45 Identities = 105/310 (33%), Positives = 170/310 (54%), Gaps = 11/310 (3%) Query: 1 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP 60 M K IA+A +TL AA PAMA + +G++ ++ NP+FV++ K + A + Sbjct: 1 MKKALIALALTTL----AAAPAMAQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLG- 55 Query: 61 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDV 120 AKV + +++ Q+ IE+ + +D++++N DS GV AVK A+ ++VVAVD Sbjct: 56 -AKVIATDAAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDA 114 Query: 121 AAAG-ADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKS 179 A+G D+ V S N AG +SC+ LA+ + GKG V I++G PV ++ RV GCK + Sbjct: 115 NASGPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVVPILQRVEGCKQALAEY 174 Query: 180 PGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIK 239 IK+++ QN R + + N++ ++P + +F++ND A+GA LA Q DIK Sbjct: 175 KDIKLVA-TQNGRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAMGA-LAAIQGSGKDIK 232 Query: 240 WISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVK 299 ++ VDGAP+A +A+ D F + AQ P +A+ A G K + V Sbjct: 233 -LTSVDGAPEAVKAIADG-GPFVETTAQFPRDQVRVGLAMALAKKWGARVVPKEVPIDVM 290 Query: 300 LITRDNVADY 309 +T+ N A + Sbjct: 291 PVTKKNAAGF 300 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: 212 Number of extensions: 11 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: 316 Length of database: 302 Length adjustment: 27 Effective length of query: 289 Effective length of database: 275 Effective search space: 79475 Effective search space used: 79475 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