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 AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 267 bits (683), Expect = 6e-76 Identities = 162/474 (34%), Positives = 269/474 (56%), Gaps = 10/474 (2%) Query: 25 VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84 ++L L +GE+ AL GENGAGKSTL I+ GL+ P+ G++ +G+ S ++A LGI Sbjct: 27 IDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEELGIR 86 Query: 85 MVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSERYGL-SVEPDALIRDI 143 MV Q L+ +V EN+ L N + G + K +K + + GL +++PD L+ ++ Sbjct: 87 MVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIAAMAQVGLDAIDPDTLVGEL 146 Query: 144 SVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIILITHKLD 203 +G QQ VEI + L +LI DEPTA+LT E+ L + + L G +II I+H+L+ Sbjct: 147 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYISHRLE 206 Query: 204 EIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEKAAAQPKDVVLEIKD 263 E+ VA RI V+R G + + + +++L LMVGR + E P+ + Sbjct: 207 ELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELG---EHIDLGPRHI--GAPA 261 Query: 264 LNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHN--K 321 L +K S KV+ +S +VR+GEI G++G+ G G+TEL++ I G DSG++ L + + Sbjct: 262 LTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADAADSGTVALGSPAQ 321 Query: 322 DITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINS 381 ++ + P + + EDR +GL+L +++ NIAL P +S G ++ + Sbjct: 322 VVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGN--MPVISSGGIVNSGDEMA 379 Query: 382 HARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEY 441 A+ ++ +R + S LSGGNQQK +I R ++R +L+ +PTRG+DVGA Sbjct: 380 LAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLLFDEPTRGIDVGAKFD 439 Query: 442 IHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQEL 495 I+ L + +GKA++V+S +L E++ + DRI V+ G++ ++ T+ +L Sbjct: 440 IYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDL 493 Score = 81.6 bits (200), Expect = 6e-20 Identities = 58/230 (25%), Positives = 109/230 (47%), Gaps = 7/230 (3%) Query: 277 GLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSV 336 G+ L + GE++ + G +G G++ L K I GL +G ++ +D + E + Sbjct: 26 GIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEELGI 85 Query: 337 GHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAG 396 V ++ + L+ ++VAEN+ L S G++ ++ A M + + Sbjct: 86 RMVMQELN---LLPTLSVAENLFLDNL----PSNGGWISRKQLRKAAIAAMAQVGLDAID 138 Query: 397 EWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAV 456 L G+QQ IAR + + +LI+ +PT L +E + +++ + + G A+ Sbjct: 139 PDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAI 198 Query: 457 LVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506 + IS L+E+ V+ RIAV+ DG + + ++L LMVG + E Sbjct: 199 IYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELGE 248 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: 644 Number of extensions: 36 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: 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 Apr 09 2024. 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