Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 198 bits (504), Expect = 2e-55 Identities = 124/361 (34%), Positives = 194/361 (53%), Gaps = 24/361 (6%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M +I++ L K + V+AV + + I G ++GPSG GK+T LR++AGLE T Sbjct: 1 MASIQLTGLKKTYAGN---VEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETIT 57 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G + D+ V+ + P +R IAMVFQN+ALYP+MTVF N+A+ LK V +++IE Sbjct: 58 DGTLKIDDRVVND-----LEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIE 112 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V + + L + L R P++LSGGQ QR A+ RALV++P L DEP SNLDA++R Sbjct: 113 RRVHDAAAMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQ 172 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R ++++QR K T+L V+HD + + ++ V+ G Q+GTP E+YE PA+ +A Sbjct: 173 MRVEIKQLQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVA 232 Query: 241 RLTGE--INLIQAKIIEN---NAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLD 295 G +N++ + N ++ +L + VIG+RPDDL + D Sbjct: 233 TFIGSPAMNMLPVAYLRERGANGLLDHLAADTD----------VIGIRPDDLRIEAPDED 282 Query: 296 KYIDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIF 355 + G V++ + GA V +D+ I A P+ G P+ + F Sbjct: 283 HLVVTGTVEL-FEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPF 341 Query: 356 D 356 + Sbjct: 342 N 342 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: 278 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: 354 Length adjustment: 29 Effective length of query: 342 Effective length of database: 325 Effective search space: 111150 Effective search space used: 111150 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