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 GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 444 bits (1141), Expect = e-129 Identities = 232/501 (46%), Positives = 335/501 (66%), Gaps = 9/501 (1%) Query: 7 IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66 I++ ++K FG AN +++ + G IH ++GENGAGKSTLM+IL G + +GEV + Sbjct: 6 IELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIH 65 Query: 67 GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILEL 126 GK I A + GIGMV QHF LV+ FTV ENIILG E + L A+K + +L Sbjct: 66 GKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKARKSLKDL 125 Query: 127 SERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMK 186 + Y L+V+PDA I +I VG QQRVEILK LYR ADILI DEPT VLTPAE +L +I+ Sbjct: 126 AAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILD 185 Query: 187 NLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFI 246 L EGK+IILITHKL EI D ++V+RRG+ TV+ + + + LAELMVGR V Sbjct: 186 RLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKVLLR 245 Query: 247 TEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAIT 306 +K A P +LEI++L++ + G +VK + L VRAGEI+G+AG+ GNGQ+EL++ + Sbjct: 246 VDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLG 305 Query: 307 GLTKVDSGSIKLHNKDI------TNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIAL 360 G+ + GSI+L+ + ++ R R+ V HVPEDR R+GL+++ EN+A Sbjct: 306 GM-REGQGSIRLNGAPLPLSGAGSDARARRAAH--VAHVPEDRQREGLIMDFHAWENVAF 362 Query: 361 QTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDR 420 ++ P + ++ + + M +FDVR W++A + SGGNQQK ++AREI+R Sbjct: 363 GYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIER 422 Query: 421 NPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQ 480 NP+LL++ QPTRG+D+GAIE+IHK++++ RD+GKA+L++S EL+EIL+++DR+AV+ DG Sbjct: 423 NPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGM 482 Query: 481 IQGIVSPETTTKQELGILMVG 501 I G + T ++ELG+LM G Sbjct: 483 IMGERPADQTDEKELGLLMAG 503 Score = 83.2 bits (204), Expect = 2e-20 Identities = 62/233 (26%), Positives = 108/233 (46%), Gaps = 16/233 (6%) Query: 276 KGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQS 335 K +S+ V G I G+ G +G G++ L+ + G K D G + +H K + Sbjct: 22 KDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIHGKRTEIPDSQAAISAG 81 Query: 336 VGHVPEDRHRDGLVLEMTVAENIALQT----YYKPPMSKYGFLDYNKINSHARELMEEFD 391 +G V + LV TV ENI L KP +SK ++L E++ Sbjct: 82 IGMVFQHFK---LVENFTVLENIILGAEDGGLLKPSLSK--------ARKSLKDLAAEYE 130 Query: 392 VRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARD 451 + + + G QQ+ I + + R D+LI+ +PT L + + + L + R Sbjct: 131 LNVDPD-ARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILDRLRA 189 Query: 452 EGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNI 504 EGK +++I+ +L EI+ +D ++V+ G++ V T+ + L LMVG + Sbjct: 190 EGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKV 242 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: 693 Number of extensions: 31 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 506 Length of database: 509 Length adjustment: 34 Effective length of query: 472 Effective length of database: 475 Effective search space: 224200 Effective search space used: 224200 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