Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate Ac3H11_2431 ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2431 Length = 514 Score = 369 bits (948), Expect = e-106 Identities = 206/510 (40%), Positives = 301/510 (59%), Gaps = 16/510 (3%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65 V+++ +TKRFG VAND ++L L +GE+ ALLGENGAGKSTLM+IL G EG + V Sbjct: 4 VLRLSHITKRFGKLVANDSISLTLARGEVLALLGENGAGKSTLMSILFGHYVADEGSIEV 63 Query: 66 KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125 G+ P A GIGMVHQHF L D TV +N++LG+E A+ K+L Sbjct: 64 FGQPLPPGQPRAALAAGIGMVHQHFTLADNLTVLDNVLLGSEPLWQPFSRRSEARAKLLA 123 Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185 +S+++GL V PDA + +SVG++QRVEILK LYRGA ILI DEPTAVLTP E L + Sbjct: 124 VSQQFGLPVSPDAKVGSLSVGERQRVEILKALYRGAHILILDEPTAVLTPQESEALFDTL 183 Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245 ++ +G SII I+HKL E+ V+ R+ V+R+GK + T +LA+ MVG ++ Sbjct: 184 AQMVAQGLSIIFISHKLGEVLRVSHRVAVLRQGKLVAEAPAQGTTQGQLAQWMVGHAIEA 243 Query: 246 ITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI 305 + A + + + +++ + G ++ +SL +RAGEIV +AG+ GNGQ L + Sbjct: 244 AERRPAQNVGEPICTLSNVSTAPA-GRDRLNDVSLTLRAGEIVAIAGVSGNGQVALADVL 302 Query: 306 TGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ---- 361 G+ +G + L + RP + Q V +PEDRH G+V ++ V EN + Sbjct: 303 CGVRAATTGQVTLRGAPL-QARPAWLVSQGVARIPEDRHAVGVVGDLPVWENAVSERLRG 361 Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREI--- 418 ++ P + ++ HA+ + E FDVRG G A SLSGGN QK I+ R + Sbjct: 362 PWFAHPWFRAFWVKRRAARQHAQRVAETFDVRGGGADAPARSLSGGNMQKLILGRALMPP 421 Query: 419 -------DRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSD 471 P L++ QPT GLD+GA+ ++ ++LI ARD G AVL+IS +LDE+L + D Sbjct: 422 QDAAGNSAPVPQLIVAHQPTWGLDIGAVMFVQQQLINARDSGAAVLLISDDLDEVLALGD 481 Query: 472 RIAVIHDGQIQGIVSPETTTKQELGILMVG 501 R+AV+HDG++ + E T++ +G+ M G Sbjct: 482 RVAVMHDGRLSEALPAEGWTREAIGLAMAG 511 Lambda K H 0.315 0.135 0.365 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: 564 Number of extensions: 26 Number of successful extensions: 10 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: 506 Length of database: 514 Length adjustment: 34 Effective length of query: 472 Effective length of database: 480 Effective search space: 226560 Effective search space used: 226560 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: 42 (22.0 bits) S2: 52 (24.6 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