Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate SM_b21438 SM_b21438 C4-dicarboxylate transport system, C4-dicarboxylate-binding protein precursor signal peptide
Query= reanno::psRCH2:GFF2082 (338 letters) >FitnessBrowser__Smeli:SM_b21438 Length = 332 Score = 190 bits (483), Expect = 4e-53 Identities = 112/320 (35%), Positives = 178/320 (55%), Gaps = 7/320 (2%) Query: 9 LAAALLGSTLSLGYAQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKASGGKLKVR 68 LAA ++ + L AA + IR G+ L + + +A+ A+EV++ + G++K+ Sbjct: 12 LAATVIAGIVGLSAHSAA--MAETTIRLGHVLADTHSWHKASTDFAKEVSEKTEGRVKIE 69 Query: 69 TFASASLGSDDQMQNAL-IGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQADQVLD 127 F S LG++ ++ + IG Q ++GS + + + + + P+ +T QA LD Sbjct: 70 IFPSGQLGTEKEVIEGMQIGTIQGGLIGS-GSFQFVEPKFGIIEMPYAWTSREQAFAALD 128 Query: 128 GPVGRQVMDKLEEKGLVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNPVFIDTFK 187 G +G + D L KG+ L +WENGFRN+TN+ PI K D G+K+RV P+ V + TF+ Sbjct: 129 GKLGTALADLLRPKGIEVLAWWENGFRNITNNKHPIVKPADLAGIKIRVTPDKVRLATFE 188 Query: 188 RMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYSPWIVTVS 247 R+GA PL F EL++AL+ D QENP + I +S FYEVQKY+S+T H++ +TVS Sbjct: 189 RLGAQPAPLAFGELYSALQQGVFDAQENPLSIIDASSFYEVQKYVSMTGHIWGAACLTVS 248 Query: 248 KRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINEVSPDEIQRMR 307 W +S +Q I+ EAA K +A+R+ + LK +GMQ NEV + Sbjct: 249 SMTWAQVSPEDQAIVKEAAVKWGNAQRQMVADNEVALIEKLKSKGMQFNEV---DKAAFV 305 Query: 308 EKAQPAIQTVIDAVGQELFD 327 + +P ++ D G EL + Sbjct: 306 DALKPIWESEKDVFGPELLE 325 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: 253 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: 332 Length adjustment: 28 Effective length of query: 310 Effective length of database: 304 Effective search space: 94240 Effective search space used: 94240 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