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 Pf1N1B4_1243 ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243 Length = 521 Score = 340 bits (873), Expect = 6e-98 Identities = 193/499 (38%), Positives = 295/499 (59%), Gaps = 8/499 (1%) Query: 7 IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66 +Q+ ++KR+ +AND ++L + GEIHALLGENGAGKSTLM I+ G+ GE+ + Sbjct: 14 LQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQ 73 Query: 67 GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILEL 126 G+ + +P++A LGIGMV QHF L + +V +NI L G K + KI E+ Sbjct: 74 GQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTP---KQLEPKIREV 130 Query: 127 SERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMK 186 S+RYG+++EP+ L+ +S+G++QRVEI++ L + +LI DEPT+VLTP E EL ++ Sbjct: 131 SQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLR 190 Query: 187 NLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFI 246 L EG SI+ I+HKL E+RA+ TV+R G+ ++++LA+LMVG + I Sbjct: 191 RLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQLMVGEAAELI 250 Query: 247 TEKAAAQPKDVVLEIKDLN-IKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI 305 T+ D L + L+ +K + DVR+GEIVGVAG+ GNGQ EL+ + Sbjct: 251 TDYPKVMGADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGVAGNGQDELLALL 310 Query: 306 TG---LTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQT 362 +G L + DS +I + + + RP + + VP +R G V E+++A+N AL T Sbjct: 311 SGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLADN-ALLT 369 Query: 363 YYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNP 422 ++ + +G + K+ + A +++ F V+ A SLSGGN QK I+ REI + P Sbjct: 370 AFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQKFILGREILQQP 429 Query: 423 DLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQ 482 LL+ + PT G+DVGA IH+ LI RD G A+LVIS +LDE+ + DR+ + GQ+ Sbjct: 430 KLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRLGALCGGQLS 489 Query: 483 GIVSPETTTKQELGILMVG 501 + + T ++G M G Sbjct: 490 PLQATVDTHLSDVGGWMAG 508 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: 620 Number of extensions: 25 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: 521 Length adjustment: 35 Effective length of query: 471 Effective length of database: 486 Effective search space: 228906 Effective search space used: 228906 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