Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 159 bits (403), Expect = 6e-44 Identities = 92/243 (37%), Positives = 144/243 (59%), Gaps = 10/243 (4%) Query: 2 IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61 I++ +SK FG+ + L ++ I EGE++ ++GPSGSGK+T LR + LE + G I Sbjct: 3 IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFG 62 Query: 62 DTEITKPKTNTLKVREN-IGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAA---QEKA 117 + ++T+ + VR+ +G VFQ++ LF H TV +N+ + + K+ + +A Q++ Sbjct: 63 NRDVTQ-----VHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRV 117 Query: 118 EDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQ 177 LL V L YP +LSGGQKQR+A+ARALA P+++L DEP ALD ++ KE+ + Sbjct: 118 SHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRR 177 Query: 178 VMKEL-VETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFL 236 ++ L E T V VTH+ A E++DRV+ M G I + P E + P S+ DFL Sbjct: 178 WLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFL 237 Query: 237 EKI 239 + Sbjct: 238 GNV 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: 183 Number of extensions: 7 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: 376 Length adjustment: 27 Effective length of query: 213 Effective length of database: 349 Effective search space: 74337 Effective search space used: 74337 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: 48 (23.1 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