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 3609577 Dshi_2961 ABC transporter related (RefSeq)
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Dino:3609577 Length = 511 Score = 336 bits (861), Expect = 1e-96 Identities = 193/498 (38%), Positives = 303/498 (60%), Gaps = 8/498 (1%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65 ++++ +TK + VAND V+ E+ +GE+HALLGENGAGKSTL+ ++ GL+ P G + Sbjct: 4 LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63 Query: 66 KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125 G P A + G+ MV QHF L +A TV ENI LG E ++ +I + Sbjct: 64 GGVPFAPPEPRAARSAGVAMVFQHFSLFEALTVAENIALGMEDPP----KMRDLAARITQ 119 Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185 +S+ YGL ++P L+ +S G++QRVEI++ L + +LI DEPT+VLTP E+ L + Sbjct: 120 VSQAYGLPLDPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILFATL 179 Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245 + L EG +I+ I+HKL+EIRA+ D T++R GK + T + +K+ +ELAE+MVG+++ Sbjct: 180 RKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKTLQQ 239 Query: 246 ITEKAAAQPKDVVLEIKDLNIKESRG-SLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304 T+ A VLE++ L+ + ++ +SL+VRAGE++G+ G+ GNGQ EL+ A Sbjct: 240 -TKSAGNAFGAPVLELRGLSQPATTPFGTPLRDISLEVRAGEVLGIGGVAGNGQDELLSA 298 Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364 I+G + + +I LH I+ P + V PE+R +M++ EN L Sbjct: 299 ISGERRAED-AIFLHGTPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTENALLTGSV 357 Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424 + +++ GFLD+ K + A ++E FDVR G +A +LSGGN QK +I RE+ + P++ Sbjct: 358 REKLTRNGFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIGREVLQRPEV 417 Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484 LIV+QPT G+D A I + L+ G AV+VIS +LDE++ +SD A ++ G++ G Sbjct: 418 LIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAALNGGRLSGK 477 Query: 485 VSPETTTKQELGILMVGG 502 V T +++G LM+GG Sbjct: 478 VPAAGLTVEQIG-LMLGG 494 Score = 87.4 bits (215), Expect = 1e-21 Identities = 67/231 (29%), Positives = 107/231 (46%), Gaps = 16/231 (6%) Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337 +S ++ GE+ + G +G G++ LVK I GL + DSG++ PR V Sbjct: 23 VSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTFGGVPFAPPEPRAARSAGVA 82 Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGE 397 V + L +TVAENIAL G D K+ A + + G Sbjct: 83 MVFQ---HFSLFEALTVAENIAL-----------GMEDPPKMRDLAARITQVSQAYGLPL 128 Query: 398 WVS--ASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKA 455 S +LS G +Q+ I R + + P LLI+ +PT L ++ + L + RDEG A Sbjct: 129 DPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILFATLRKLRDEGTA 188 Query: 456 VLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506 +L IS +L+EI + D ++ G++ P + +EL +MVG + + Sbjct: 189 ILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKTLQQ 239 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: 580 Number of extensions: 25 Number of successful extensions: 8 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: 511 Length adjustment: 34 Effective length of query: 472 Effective length of database: 477 Effective search space: 225144 Effective search space used: 225144 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