Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB
Query= SwissProt::P54537 (240 letters) >NCBI__GCF_000012965.1:WP_011373501.1 Length = 261 Score = 142 bits (357), Expect = 8e-39 Identities = 87/246 (35%), Positives = 142/246 (57%), Gaps = 13/246 (5%) Query: 2 IKVEKLSKSFGKHEV--LKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEK--PNG-- 55 ++V+ ++ K +V +K +S +A+ + A+IGPSG GK+T LR N + PN Sbjct: 13 LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYPNNKY 72 Query: 56 -GTITIKDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQ 114 G IT KD I K + +K+R IGM+FQ FP ++ +N+ Y +++ Sbjct: 73 SGEITFKDRNILTSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYGLKLQGIKNRTELS 131 Query: 115 EKAEDLLRKVGLFEKRNDY----PNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPE 170 + E L+ ++ + D N LSGGQ+QR+ IARA+A+ P+++LFDEPTSALDP Sbjct: 132 GRVEKALKDAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLFDEPTSALDPI 191 Query: 171 MVKEVLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSK 230 + +++ EL E ++++IVTH M A V+D FM G ++E G +E F++PK K Sbjct: 192 STGGIEELIVELRER-VSIIIVTHNMQQAARVSDYTGFMYLGELIELGKTEEIFVTPKEK 250 Query: 231 RAQDFL 236 ++++ Sbjct: 251 LTEEYI 256 Lambda K H 0.317 0.134 0.368 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: 163 Number of extensions: 9 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: 240 Length of database: 261 Length adjustment: 24 Effective length of query: 216 Effective length of database: 237 Effective search space: 51192 Effective search space used: 51192 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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