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 RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 390 bits (1003), Expect = e-113 Identities = 224/509 (44%), Positives = 307/509 (60%), Gaps = 14/509 (2%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65 ++++ +TKRFG VAND ++LEL++GE+ ALLGENGAGKSTL++IL G G V V Sbjct: 5 ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64 Query: 66 KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125 G+ P A GIGMVHQHF L D +V +NI+LG + LD A+ K+L Sbjct: 65 DGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLA 124 Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185 L+ER+GL+V P A + ++SVG++QRVEI+K LYRGA +LI DEPTAVLTP E L + Sbjct: 125 LAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTL 184 Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245 LI EG S+I I+HKLDE+ V+DRI V+R GK + T ELAELMVGR V+ Sbjct: 185 AQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVAM 244 Query: 246 ITEKAAAQPKD--------VVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNG 297 A +D VL ++ + + + G ++ +SL VRAGEIVG+AG+ GNG Sbjct: 245 PERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSGNG 304 Query: 298 QTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAEN 357 Q L + +G+ + G I L K + + +PR V VPEDRH G+V ++ V EN Sbjct: 305 QAALAELASGMLEASEGRITLAGKPM-SAKPRAWIGAGVARVPEDRHAIGVVGDLAVWEN 363 Query: 358 IALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIARE 417 + +P S++G + AR+L+ FDVR AG V A ++SGGN QK I+ R Sbjct: 364 AVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILGRA 423 Query: 418 ID-----RNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDR 472 + P L++ SQPT GLD+GA+ Y+ RL+ A EG AVL+IS +LDE+ ++DR Sbjct: 424 LSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALADR 483 Query: 473 IAVIHDGQIQGIVSPETTTKQELGILMVG 501 IAV+H G + T ELG+ M G Sbjct: 484 IAVMHAGHLTEARPTAAWTLGELGLAMAG 512 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: 679 Number of extensions: 28 Number of successful extensions: 8 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: 530 Length adjustment: 35 Effective length of query: 471 Effective length of database: 495 Effective search space: 233145 Effective search space used: 233145 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