Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein (TIGR)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__DvH:208681 Length = 349 Score = 192 bits (489), Expect = 9e-54 Identities = 123/358 (34%), Positives = 198/358 (55%), Gaps = 21/358 (5%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M+TI ++ +S+ + +V+AVD+VS ++ G +LGPSG GK+T LRLIAGLE T Sbjct: 1 MSTIVLDKVSRHWG----DVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVT 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 SG I V++ + P +R +AMVFQ++AL+P++TV DNI F L + KVP + + Sbjct: 57 SGRILIGGRDVTN-----LPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQ 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 ++ E LGL +L R P ELSGGQ QR A+ RALV + V L+DEP SNLDA++R+ Sbjct: 112 KRLDRAVEILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQE 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R +R +Q+ +T + V+HD + ++A++ ++ G+ Q TPTE+Y PAT Sbjct: 172 MRREIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAG 231 Query: 241 RLTG--EINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYI 298 G +NL++ + ++ +A + + ++ ++G+RP+ + + D Sbjct: 232 SFIGTPPMNLVRLQGNDDGIRVAGSR--SGRVTCHAGADCMLGIRPEHIRIVD------- 282 Query: 299 DMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFD 356 D V+ V Y G ++ + E + ++V G E +L V IFD Sbjct: 283 DGWRAVVESVEY-LGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFD 339 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: 216 Number of extensions: 4 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: 349 Length adjustment: 29 Effective length of query: 342 Effective length of database: 320 Effective search space: 109440 Effective search space used: 109440 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 Apr 09 2024. 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