Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 195 bits (496), Expect = 1e-54 Identities = 121/358 (33%), Positives = 198/358 (55%), Gaps = 21/358 (5%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M+ I++ N+S+ + +V+AVD+VS ++ G +LGPSG GK+T LRLIAGLE T Sbjct: 1 MSAIQLLNVSRHWG----DVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVT 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 SG I V+ + P +R +AMVFQ++AL+P++TV +NI F L + KVP+ + E Sbjct: 57 SGRIMIGERDVTH-----LPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAERE 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 ++ + LGLS +L R P ELSGGQ QR A+ RALV + V L+DEP SNLDA++R Sbjct: 112 KRLTRAVDILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHE 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R +R +Q+ +T + V+HD + ++A++ ++ G+ Q TP+E+Y PAT Sbjct: 172 MRREIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAG 231 Query: 241 RLTG--EINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYI 298 G +NL++ + +A + + + ++ V+G+RP+ + + Sbjct: 232 NFIGTPPMNLVRLDDARGSVCVAGSR--SGTVSVVDSADYVLGIRPEHIRIVP------- 282 Query: 299 DMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFD 356 + V+ V Y G ++ + E + ++VD + G E +L + IFD Sbjct: 283 EGWRAVVESVEY-LGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHIHIFD 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: 234 Number of extensions: 10 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: 371 Length of database: 350 Length adjustment: 29 Effective length of query: 342 Effective length of database: 321 Effective search space: 109782 Effective search space used: 109782 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