Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__azobra:AZOBR_RS23525 Length = 269 Score = 254 bits (650), Expect = 9e-73 Identities = 135/245 (55%), Positives = 168/245 (68%), Gaps = 5/245 (2%) Query: 1 MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60 +I++ + KSFG EVLK++S T+ VIGPSGSGKST LRC N LE + G I I Sbjct: 1 VIEIRNVYKSFGSTEVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIRI 60 Query: 61 KDTEITK-----PKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQE 115 I P +R GMVFQ F+LFPH T +EN+M APV V+ +K A+E Sbjct: 61 NHRTIIADGKPLPDKELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAKAEARE 120 Query: 116 KAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEV 175 A +LLRKVGL +K + YP+ LSGGQKQR AIARALAM P +MLFDEPTSALDPE+V EV Sbjct: 121 LAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPELVGEV 180 Query: 176 LQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDF 235 LQVMK L E GMTM++VTHEMGFA+EVAD V+ M G IVE G+P++ F +P +R + F Sbjct: 181 LQVMKTLAEEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQERTRGF 240 Query: 236 LEKIL 240 L ++ Sbjct: 241 LRALV 245 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: 203 Number of extensions: 6 Number of successful extensions: 2 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: 269 Length adjustment: 24 Effective length of query: 216 Effective length of database: 245 Effective search space: 52920 Effective search space used: 52920 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: 47 (22.7 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