Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_111609142.1 DK187_RS20415 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_003259225.1:WP_111609142.1 Length = 371 Score = 211 bits (538), Expect = 2e-59 Identities = 130/374 (34%), Positives = 205/374 (54%), Gaps = 28/374 (7%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M ++++ N+ K F V + + + I G ++G SG GK+T LRL++GLE+ T Sbjct: 1 MASVKLNNIKKRFGN----VDVLHGIDLDIKDGEFVVLIGESGCGKSTLLRLLSGLEDIT 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G +Y D+E V+ SP KRGIAMVFQ++ALYP+M VF N+AF LK++ K + Sbjct: 57 EGDLYIDDERVNG-----RSPAKRGIAMVFQSYALYPHMNVFKNMAFGLKISGKDKAFVN 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 NKV E +++L + +L R P+ELSGGQ QR AI RA+V+DPKV L DEP SNLDA +R Sbjct: 112 NKVMEAAKKLKIDHLLERLPRELSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDASLRVQ 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R + K+ +E K T + V+HD + + +K V+ G+ Q+G P ++Y +P T +A Sbjct: 172 TRVELGKLHQELKATVVYVTHDQVEAMTLGDKIVVMNKGRVEQVGAPLDLYHHPKTQFVA 231 Query: 241 RLTG--EINLIQAKI----IENNAIIAN----LKVPLNNMELKGQSNIVIGLRPDDLTLS 290 G ++N + AKI EN I+ ++ +++ L + +GLRP+ + L Sbjct: 232 GFIGSPKMNFLNAKIHHSDPENTQIMLESGRVIQASIDSSSLNKGDIVKLGLRPEHIAL- 290 Query: 291 DTLLDKYIDMGIVK--VKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAK 348 + D V+ V L+ + + + V + + + VD + + G + Sbjct: 291 ------HCDNNTVEGTVTLIEHLGELSYLYVDIGQEGEMVLKVDGDNQHQAGDNITFGIQ 344 Query: 349 PNKVKIFDLNGSNL 362 PN + +FD G L Sbjct: 345 PNHLYLFDHQGKAL 358 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: 323 Number of extensions: 13 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: 371 Length adjustment: 30 Effective length of query: 341 Effective length of database: 341 Effective search space: 116281 Effective search space used: 116281 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 24 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