Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 197 bits (501), Expect = 4e-55 Identities = 102/264 (38%), Positives = 161/264 (60%), Gaps = 12/264 (4%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M T+ +L+K F AVD + + + +LGPSG GKTT LRLIAGLE PT Sbjct: 1 MATVETRSLTKRFDG----TNAVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPT 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 SG I V+ + P +AMVFQ++ALYP+++V NIAFPL+ ++P++ I Sbjct: 57 SGDILVGGRVVTG-----LPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIA 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 KV + G+ +L+R P++LSGG+ QR A+ARA+V++P LLDEP SNLDA++R S Sbjct: 112 RKVSWAAALFGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTS 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 AR ++++QR TT+ V+HD + A+ ++ ++ +G+ Q+GTP ++YE PA +A Sbjct: 172 AREELQQLQRRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVA 231 Query: 241 RLTGEINLIQAKIIENNAIIANLK 264 G + +++ +A++ + Sbjct: 232 TFIGSPPM---NLVDTDALVTGFR 252 Lambda K H 0.317 0.136 0.374 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: 295 Number of extensions: 10 Number of successful extensions: 2 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: 371 Length of database: 351 Length adjustment: 29 Effective length of query: 342 Effective length of database: 322 Effective search space: 110124 Effective search space used: 110124 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