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 3609460 Dshi_2844 inner-membrane translocator (RefSeq)
Query= TCDB::A2RKA6 (364 letters) >FitnessBrowser__Dino:3609460 Length = 372 Score = 170 bits (430), Expect = 6e-47 Identities = 115/363 (31%), Positives = 191/363 (52%), Gaps = 8/363 (2%) Query: 8 VLVPLIAIVFGFLLGAIIMLAFGYNPIWGYEDLFISALGSARSIGETLQTMGPLILTALS 67 +LVPL++++ F++ ++++A G NP + + ALGS G TL I T L+ Sbjct: 11 LLVPLLSVLIAFVISGLVIIAIGENPWEALKLMVTGALGSTYGWGYTLYYATNFIFTGLA 70 Query: 68 FAVAMKVGLFNIGMSGQALAGWISSMWFALSFPDIPRLLMIPLVVIIGMVFGAFMGFIPG 127 AVA +FNIG GQA+ G + L P + +P VI G VFGA IP Sbjct: 71 VAVAFHARMFNIGGEGQAMLGGLGVALICLYIPWPHWAMALPAAVIGGAVFGAAWAAIPA 130 Query: 128 ILRALLGTSEVITTIMLNYIMLFFSTFMIHSMFQKNILMDNTT----DQTKLISANASFR 183 L+A G+ VITTIM N+I +++ + + MD +T + T L + + Sbjct: 131 YLQAKRGSHIVITTIMFNFIGAAVLNYLLVNQLRPQGSMDPSTAKFPEATHLPTLHDLLA 190 Query: 184 TNWMSSLTDNSTLNIGLIIAIIALVIMAIIFTKTTLGFEIKAVGLNPDASEYAGISAKRT 243 + + + +NI L++A++A + ++ +T LG+EI+A G + A+ YAGIS + Sbjct: 191 PLGI-EFSRAAPVNISLLVALVACYLFWLLIWRTKLGYEIRAYGNSETAAVYAGISPTKI 249 Query: 244 LILSMVVAGALAGLGGVVYGFGYMQNFVSQSASLDIGFYGMAVALLGGNSPIGILFAALL 303 ++++M+++G LAG+ + G + V + GF G+AVAL+G + P+G+L AA+L Sbjct: 250 IMVAMLISGGLAGMMAINNVMGEAERLVLNAVE-GAGFIGIAVALMGRSHPVGVLLAAIL 308 Query: 304 FSVL-QTGAPGMTNDGIPPEIVKVVTAAIIFFI-AVKFIIEVMLPKAKAIKASEATKKKG 361 F L Q GA IP E++ V+ A +I F A+ ++ + + KA T ++ Sbjct: 309 FGFLYQGGAELALWTNIPRELIVVIQALVILFTGALDNMVRMPIEKAFLAAHRRKTARRS 368 Query: 362 EKA 364 E A Sbjct: 369 EPA 371 Lambda K H 0.327 0.141 0.404 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: 302 Number of extensions: 13 Number of successful extensions: 3 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: 364 Length of database: 372 Length adjustment: 30 Effective length of query: 334 Effective length of database: 342 Effective search space: 114228 Effective search space used: 114228 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 (21.7 bits) S2: 49 (23.5 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