Align Basic membrane lipoprotein, 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 AZOBR_RS06620 AZOBR_RS06620 membrane protein
Query= TCDB::D2BKA1 (350 letters) >FitnessBrowser__azobra:AZOBR_RS06620 Length = 330 Score = 160 bits (406), Expect = 3e-44 Identities = 115/353 (32%), Positives = 173/353 (49%), Gaps = 39/353 (11%) Query: 4 RVIAVSALALASVAVLAGCRSHDAAGSGKAKTDLKAAIVTDTGGVNDRSFNQSAWEGLQS 63 R++A+ AL+L + V AAG A + A+V D GG D+SFN++A+ G + Sbjct: 3 RILAILALSLTAATV-------PAAGPALAADEFMPAVVFDQGGKFDKSFNEAAYNGAER 55 Query: 64 WGKENNLKKGTGYTYFQSNSASDYTTNYNSAEQQGYKLLFGIGFSLQDATSAAAKNNPKS 123 + KE G Y F+ S S + ++G ++ +GFS A ++ P + Sbjct: 56 FKKET----GIVYREFEVTSESQREQALRNMARRGATVITAVGFSQSAAVDKVSREYPNT 111 Query: 124 NFVIVDSVIKDQKNVASATFADNESAYLAGVAAAKATKTNKIGFIGGMQSDVITRFEKGY 183 F ++D + D NV S TF ++E ++L G+ AA A+++ K+GFIGGM +I F GY Sbjct: 112 KFCLIDDKL-DLPNVQSVTFKEHEGSFLVGMLAALASQSGKVGFIGGMDIPLIRNFLTGY 170 Query: 184 EAGAKSVNPDIKVDVQYAG----SFSDAAKGKTIAAAMYGAGDDVVYQCAGGVGTGVFSE 239 E G K V D +V G +++D +G +A + +G G DVV+ AG G GV Sbjct: 171 EQGVKHVKADGEVFTNMTGTTPAAWNDPTRGAELAKSQFGRGADVVFAAAGATGLGVLQA 230 Query: 240 AKALNSTKNEADKVWVIGVDQDQEYLGKYKSKDGKDSNFVLVSTIKEVGNVVKDIADKTK 299 A +A K+ V GVD +Q ++ K +L S +K V V D K Sbjct: 231 AA-------DAGKLGV-GVDSNQNWIHPGK---------ILTSMVKRVDVTVYDCMKSAK 273 Query: 300 DGKFPGGTIVTYDLKNGGVNLGLDSAN-----SEIKDAVAKAKADIIDGKITV 347 DG + G V LK GV LD N +E++ AV AK II G++ V Sbjct: 274 DGSWTAGHRVV-GLKEEGVGYALDENNRKLVTAEMEKAVEDAKRKIIAGELAV 325 Lambda K H 0.310 0.128 0.353 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: 271 Number of extensions: 16 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: 350 Length of database: 330 Length adjustment: 28 Effective length of query: 322 Effective length of database: 302 Effective search space: 97244 Effective search space used: 97244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 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