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 GFF1355 Psest_1390 Uncharacterized ABC-type transport system, permease component
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__psRCH2:GFF1355 Length = 308 Score = 154 bits (389), Expect = 3e-42 Identities = 99/294 (33%), Positives = 154/294 (52%), Gaps = 19/294 (6%) Query: 14 MLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPWLSIL 73 M+ TPL+ ++G + E+ G++N+G EG+M GA + F S WL +L Sbjct: 13 MIRTGTPLLLVALGELVCEKSGVLNLGQEGMMLFGAVIGFIV------AFASGNLWLGVL 66 Query: 74 FGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININEQIGY 133 F L G L S L A+ + A+ + +G L + L F+ G + + + Sbjct: 67 FACLAGVLLSLLFAMVALGFNANQVATGLALTIFGVGLSSFV-------GASWVGKPLAG 119 Query: 134 WN---VPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQAA 190 + +PLLS IPVIG++ F Q L + A++AW VL K+R GL +++VGENP AA Sbjct: 120 FEPIAIPLLSEIPVIGRMLFAQDLLVYLSFGLFALVAW-VLLKSRIGLIIQAVGENPNAA 178 Query: 191 DTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWNP 250 +G+ V R V+ G + G+ G + A + ++ + AG+G+I+LA ++F W Sbjct: 179 SAMGLPVLRVRTLAVMFGGAMAGLAGGYMSLAYTPMWAENMTAGRGWIALALVVFASWRV 238 Query: 251 IGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLALFLGKAI 304 +L + LFGL + L +V Q G+ IP + L M PYV TI+VL L AI Sbjct: 239 SRVLLGAYLFGLASILHLV-AQGLGL-AIPGNLLAMLPYVATILVLVLLSRDAI 290 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: 278 Number of extensions: 19 Number of successful extensions: 5 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: 308 Length adjustment: 27 Effective length of query: 290 Effective length of database: 281 Effective search space: 81490 Effective search space used: 81490 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