Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_041670877.1 RSPH17029_RS18130 amino acid ABC transporter ATP-binding protein
Query= SwissProt::P54537 (240 letters) >NCBI__GCF_000015985.1:WP_041670877.1 Length = 242 Score = 258 bits (659), Expect = 7e-74 Identities = 131/240 (54%), Positives = 173/240 (72%) Query: 1 MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60 MI++ +SK +G +VL ++S + +GE V V GPSGSGKST +RC+N LE G I + Sbjct: 1 MIRMSHVSKWYGHFQVLHDVSLDVRKGERVVVCGPSGSGKSTLIRCINRLEVHQSGQIFV 60 Query: 61 KDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDL 120 K E+T N +R +IGMVFQ+F+LFPH TVLEN+ P+ ++ K AA++ A Sbjct: 61 KGLEMTDNVKNIDTIRRHIGMVFQNFNLFPHLTVLENLTLGPMLTRQMKKSAAEDLAMHF 120 Query: 121 LRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMK 180 LRKV + E+ YP +LSGGQ+QRVAIAR+L M P+IMLFDEPTSALDPEM+KEVL M Sbjct: 121 LRKVRIPEQSGKYPLQLSGGQQQRVAIARSLCMEPEIMLFDEPTSALDPEMIKEVLDTMI 180 Query: 181 ELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKIL 240 EL E+GMTM++VTHEMGFA+ VAD V+FM G VE G P+EFF +P+ +R + FL++IL Sbjct: 181 ELAESGMTMIVVTHEMGFARTVADNVVFMADGRKVESGPPEEFFGNPREERTRAFLDQIL 240 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: 192 Number of extensions: 8 Number of successful extensions: 1 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: 242 Length adjustment: 23 Effective length of query: 217 Effective length of database: 219 Effective search space: 47523 Effective search space used: 47523 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