Align Purine/cytidine ABC transporter permease 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 RR42_RS30790 RR42_RS30790 ABC transporter permease
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__Cup4G11:RR42_RS30790 Length = 321 Score = 145 bits (365), Expect = 2e-39 Identities = 95/306 (31%), Positives = 156/306 (50%), Gaps = 22/306 (7%) Query: 14 MLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPWLSIL 73 +L +TPLIF ++G + ER G++N+G+EGIM GAFS + ++ W + Sbjct: 17 VLRVATPLIFGTLGVLLCERAGVLNLGIEGIMVAGAFSGWL------AVYHGAPLWGGVA 70 Query: 74 FGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININEQ--- 130 A +G F LH TV+L V+G + ++A +L + Y+ G +++ Sbjct: 71 VAAGVGLAFGLLHGWLTVSLALSQHVAGLGVTMLATSLSYYA----YRLGFASVSTPPTI 126 Query: 131 IGYWNVPLLSNIPVIG----KIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGEN 186 + + + +P+IG +F +T+L +V ++AW +L++T GL +R VGEN Sbjct: 127 TPFAPMHWIGGVPLIGGMFSPVFGEETALTLLALGLVPVVAW-LLYRTPLGLAVRMVGEN 185 Query: 187 PQAADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFG 246 P AA+ GI V A R ++ L VGGA + F + I G+G+I +A ++F Sbjct: 186 PAAAEGQGIRVGATRIGAIMAGSALMAVGGAFLTLSAFNAFFFNMINGRGWICVALVVFA 245 Query: 247 KWNPIGAMLSSLLFGLFTSLAV----VGGQIPGIKEIPSSFLQMAPYVFTIIVLALFLGK 302 W P A+ +LLF F +L + G +PG+ +P M PYV +I+ L L + Sbjct: 246 SWRPGRALAGALLFAAFDALQLRLQQSGASLPGLPPLPYQLYLMLPYVLSILALVLVARR 305 Query: 303 AIAPKA 308 A P+A Sbjct: 306 AAYPQA 311 Lambda K H 0.326 0.142 0.419 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: 295 Number of extensions: 21 Number of successful extensions: 4 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: 317 Length of database: 321 Length adjustment: 28 Effective length of query: 289 Effective length of database: 293 Effective search space: 84677 Effective search space used: 84677 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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