Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate 16031 b1917 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__Keio:16031 Length = 250 Score = 263 bits (672), Expect = 2e-75 Identities = 137/245 (55%), Positives = 174/245 (71%), Gaps = 6/245 (2%) Query: 2 IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61 I+V+ L K F VL I + GEVVA+IGPSGSGK+T LR +NLLE+P GTIT+ Sbjct: 4 IEVKNLVKKFHGQTVLHGIDLEVKPGEVVAIIGPSGSGKTTLLRSINLLEQPEAGTITVG 63 Query: 62 DTEI------TKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQE 115 D I ++ K+ ++R+++G VFQ+F+LFPH+TVLENI+ PV VK E K+ A Sbjct: 64 DITIDTARSLSQQKSLIRQLRQHVGFVFQNFNLFPHRTVLENIIEGPVIVKGEPKEEATA 123 Query: 116 KAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEV 175 +A +LL KVGL K YP RLSGGQ+QRVAIARALAM P+++LFDEPTSALDPE+V EV Sbjct: 124 RARELLAKVGLAGKETSYPRRLSGGQQQRVAIARALAMRPEVILFDEPTSALDPELVGEV 183 Query: 176 LQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDF 235 L +++L + TMVIVTHEM FA++VADR +FMDQG IVE G K F P+ R + F Sbjct: 184 LNTIRQLAQEKRTMVIVTHEMSFARDVADRAIFMDQGRIVEQGAAKALFADPEQPRTRQF 243 Query: 236 LEKIL 240 LEK L Sbjct: 244 LEKFL 248 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: 189 Number of extensions: 3 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: 250 Length adjustment: 24 Effective length of query: 216 Effective length of database: 226 Effective search space: 48816 Effective search space used: 48816 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 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