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 WP_002878343.1 B506_RS03315 BMP family ABC transporter substrate-binding protein
Query= TCDB::D2BKA1 (350 letters) >NCBI__GCF_000387565.1:WP_002878343.1 Length = 365 Score = 317 bits (812), Expect = 3e-91 Identities = 158/351 (45%), Positives = 229/351 (65%), Gaps = 6/351 (1%) Query: 3 KRVIAVSALALASVAVLAGCRSHDAAGSGKAKTDLKA-AIVTDTGGVNDRSFNQSAWEGL 61 K++ ++ A++ +L C+ ++ S KT + A++TD ++D SFN++AW G Sbjct: 7 KKLATIATAAVSVSVLLTACQGKKSSSSTGTKTTKHSIALITDNNAIDDHSFNEAAWNGF 66 Query: 62 QSWGKENNLKKGTG-YTYFQSNSASDYTTNYNSAEQQGYKLLFGIGFSLQDATSAAAKNN 120 +++GK++ LK+G G Y YF+S+SA+D+T N N A G++ +FG+G+ L A +AAK N Sbjct: 67 KAFGKKHGLKQGKGGYQYFESSSAADFTPNANEAASSGFETIFGVGYQLTSAIKSAAKKN 126 Query: 121 PKSNFVIVDSVIKDQKNVASATFADNESAYLAGVAAAKATKTNKIGFIGGMQSDVITRFE 180 PK NFVI+D VI QKNVAS TF N+++YLAG+AAA TKTN +G+IGG +S + FE Sbjct: 127 PKKNFVIIDDVISGQKNVASVTFESNQASYLAGIAAAYTTKTNHVGYIGGAKSATLELFE 186 Query: 181 KGY----EAGAKSVNPDIKVDVQYAGSFSDAAKGKTIAAAMYGAGDDVVYQCAGGVGTGV 236 G+ EAGAK++ IK+D QY G+F+ K K+IA +MY +G D++Y AG G GV Sbjct: 187 AGFKQGVEAGAKALGKKIKIDDQYIGNFTSTDKAKSIAQSMYASGADIIYHAAGNAGNGV 246 Query: 237 FSEAKALNSTKNEADKVWVIGVDQDQEYLGKYKSKDGKDSNFVLVSTIKEVGNVVKDIAD 296 F+EAK +N + + KVWVIGVD DQ LG Y SKDGK SNFVL S +K + V+ IA+ Sbjct: 247 FTEAKDINKNRKASKKVWVIGVDVDQSSLGSYTSKDGKKSNFVLTSVLKGLDVAVERIAE 306 Query: 297 KTKDGKFPGGTIVTYDLKNGGVNLGLDSANSEIKDAVAKAKADIIDGKITV 347 K GKFPGG Y L+ GV++ + +S+ V A+ I++GK+ V Sbjct: 307 KAYQGKFPGGKHFVYTLEGNGVSVTKGNIDSKTWSKVQAARKQILNGKVKV 357 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: 417 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 350 Length of database: 365 Length adjustment: 29 Effective length of query: 321 Effective length of database: 336 Effective search space: 107856 Effective search space used: 107856 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 24 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