Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 197 bits (501), Expect = 4e-55 Identities = 109/277 (39%), Positives = 166/277 (59%), Gaps = 20/277 (7%) Query: 23 VDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSPE 82 V++ +TI +LGPSG GKTT +R+IAGLEEP+SG I+ + V++ + P+ Sbjct: 19 VEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSGEIWIGDRMVNA-----LDPK 73 Query: 83 KRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVLNRYPKE 142 R +AMVFQ++ LYPNM V++NI FPLK+ KVP+ + E +V S + L L+R P Sbjct: 74 DRDVAMVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEARVMRASAMVELDDFLHRKPAA 133 Query: 143 LSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVSHD 202 LSGGQ QR A+ARA+V++P V L+DEP SNLDA++R S RA ++ + E ++TT+ V+HD Sbjct: 134 LSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNLSHELQVTTIYVTHD 193 Query: 203 PADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGE--INLIQAKIIE----- 255 + +A++ V+ G Q+GTP EIY+ PA +A G +NL++ + + Sbjct: 194 QIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFIGSPAMNLMEGAVTDGTFHG 253 Query: 256 NNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDT 292 + IA L + +G R +D + D+ Sbjct: 254 DRVAIAGLS--------GAAGRVTLGFRAEDAQVVDS 282 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: 291 Number of extensions: 7 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: 347 Length adjustment: 29 Effective length of query: 342 Effective length of database: 318 Effective search space: 108756 Effective search space used: 108756 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