Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= TCDB::P73721 (252 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 257 bits (657), Expect = 4e-73 Identities = 139/252 (55%), Positives = 181/252 (71%), Gaps = 8/252 (3%) Query: 8 LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67 +I D L K FG ++VL+GV+ DVIS+IG SG GKST LRC+N LE GR+ V Sbjct: 415 MIEVDGLHKRFGNIEVLKGVSLTAREGDVISLIGASGSGKSTLLRCINMLEVPDQGRILV 474 Query: 68 AG------VDLSGAKI--DQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIP 119 G D GA + D K L ++R +GMVFQ+FNL+PH TVL+NL+ AP +VLR Sbjct: 475 DGESIQLNFDRPGAPLVSDAKQLVRIRSSLGMVFQNFNLWPHRTVLENLIEAPTQVLRES 534 Query: 120 MAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDP 179 AEA +RA L++VGL K + YP LSGGQ+QRVAIAR L M+P+++LFDEPTSALDP Sbjct: 535 RAEATERAEALLERVGLAAKRNEYPAFLSGGQQQRVAIARALAMRPKVMLFDEPTSALDP 594 Query: 180 ELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKS 239 ELVGEVL V++ LAEEG TM +VTHEM FAR+VS++V + +QG+IEE G P+EVF +P+S Sbjct: 595 ELVGEVLRVIRSLAEEGRTMILVTHEMAFARDVSSKVAYLHQGLIEEAGSPDEVFVHPRS 654 Query: 240 DRLRAFLSRIQS 251 +R R F++ Q+ Sbjct: 655 ERCRQFVNAHQT 666 Lambda K H 0.321 0.139 0.397 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: 387 Number of extensions: 13 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: 252 Length of database: 667 Length adjustment: 31 Effective length of query: 221 Effective length of database: 636 Effective search space: 140556 Effective search space used: 140556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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