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 AO356_07975 AO356_07975 ABC transporter
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07975 Length = 517 Score = 331 bits (848), Expect = 4e-95 Identities = 189/499 (37%), Positives = 294/499 (58%), Gaps = 8/499 (1%) Query: 7 IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66 +Q+ ++KR+ +AND ++L ++ GEIHALLGENGAGKSTLM I+ G+ GEV + Sbjct: 10 LQLRKISKRYPGCLANDAIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTPADSGEVIWQ 69 Query: 67 GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILEL 126 G+ N+ +P++A +LGIGMV QHF L + TV +NI L T G L + +I E+ Sbjct: 70 GQRVNLRNPAQARSLGIGMVFQHFSLFETLTVAQNIALAMGATAGSPAQL---EPRIREV 126 Query: 127 SERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMK 186 S RYG+++EP L+ +S+G++QRVEI++ L + +LI DEPT+VLTP E EL ++ Sbjct: 127 SRRYGMALEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPVEAEELFVTLR 186 Query: 187 NLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFI 246 L EG SI+ I+HKL E+RA+ TV+R G+ +++ELA+LMVG + I Sbjct: 187 RLASEGCSILFISHKLGEVRALCHSATVLRGGRVSGHCTPAHCSDRELAQLMVGEAAGLI 246 Query: 247 TEKAAAQPKDVVLEIKDLN-IKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI 305 T+ L+I L+ ++ + L+V +GEIVG+AG+ GNGQ E + + Sbjct: 247 TDYPKVSADKAFLQINKLSWHNPDPFGCSLRDIDLEVCSGEIVGIAGVAGNGQDEWLALL 306 Query: 306 TGLTKV---DSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQT 362 +G T++ +I+ + + + RP + VP +R G V ++++A+N AL + Sbjct: 307 SGETQLPRQHGETIRFAGQPVAHLRPDARRRLGLAFVPAERLGHGAVPQLSLADN-ALLS 365 Query: 363 YYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNP 422 ++ + +G + ++ A E++ F V+ A SLSGGN QK I+ REI + P Sbjct: 366 AFQQGLVSHGLIRRRQVEHLAEEIIRRFGVKTPDTRTPARSLSGGNLQKFILGREILQQP 425 Query: 423 DLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQ 482 LL+ + PT G+DVGA IH+ LI RD G A+LVIS +LDE+ +SDR+ + G++ Sbjct: 426 KLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGRLS 485 Query: 483 GIVSPETTTKQELGILMVG 501 + T ++G M G Sbjct: 486 ALRPTGETRLSDVGGWMAG 504 Score = 40.4 bits (93), Expect = 2e-07 Identities = 49/229 (21%), Positives = 100/229 (43%), Gaps = 14/229 (6%) Query: 25 VNLELKKGEIHALLGENGAGKSTLMNILSG--LLEPSEGE-VHVKGKLENIDSPSKAANL 81 ++LE+ GEI + G G G+ + +LSG L GE + G+ P L Sbjct: 279 IDLEVCSGEIVGIAGVAGNGQDEWLALLSGETQLPRQHGETIRFAGQPVAHLRPDARRRL 338 Query: 82 GIGMVHQHFM---LVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSE----RYGLSV 134 G+ V + V ++ +N +L + +G+ ++++ L+E R+G+ Sbjct: 339 GLAFVPAERLGHGAVPQLSLADNALL-SAFQQGLVSHGLIRRRQVEHLAEEIIRRFGVKT 397 Query: 135 EPDALI--RDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEG 192 PD R +S G Q+ + + + + +L+ PT + + + + L G Sbjct: 398 -PDTRTPARSLSGGNLQKFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIALRDAG 456 Query: 193 KSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR 241 +I++I+ LDE+ ++DR+ + G+ G+ ++ M G+ Sbjct: 457 AAILVISEDLDELFQISDRLGALCGGRLSALRPTGETRLSDVGGWMAGQ 505 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: 603 Number of extensions: 26 Number of successful extensions: 9 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: 517 Length adjustment: 35 Effective length of query: 471 Effective length of database: 482 Effective search space: 227022 Effective search space used: 227022 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