Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 Length = 341 Score = 209 bits (531), Expect = 1e-58 Identities = 118/310 (38%), Positives = 188/310 (60%), Gaps = 26/310 (8%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M +++ENL K + E+ AV +++++ G +LGPSG GKTT L++IAG E + Sbjct: 1 MAFVQLENLGKRYG----EIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVS 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 SG I D ++ + P RG+ +VFQ++AL+P+MTV DN+AF L++ KVP D+++ Sbjct: 57 SGRIVLDGRDITHAK-----PASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQ 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V V + + L+ RYP+ELSGGQ QR A+ARALV +P VLLLDEP SNLDA +RE Sbjct: 112 QRVDRVLKLVRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREE 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 + +R+IQRE +TTL+V+HD ++ +I+++ V+ G+ QI P +YE+P T+ I+ Sbjct: 172 MQFEIRRIQREVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFIS 231 Query: 241 RLTGEINLIQAKIIENNAI-IANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYID 299 G+ NL+ + + + N + + + LRP+ + L D + Sbjct: 232 GFVGKANLLPGERDSAGVVQVCN----------RDNGELTLSLRPEKIDLRD------VG 275 Query: 300 MGIVKVKLVS 309 +G ++ K+VS Sbjct: 276 LGRLQGKIVS 285 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: 282 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: 341 Length adjustment: 29 Effective length of query: 342 Effective length of database: 312 Effective search space: 106704 Effective search space used: 106704 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