Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate AO353_12660 AO353_12660 histidine ammonia-lyase
Query= curated2:A9WHT8 (523 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12660 Length = 514 Score = 266 bits (679), Expect = 2e-75 Identities = 189/506 (37%), Positives = 265/506 (52%), Gaps = 24/506 (4%) Query: 13 LTIEQVLAVAYGQPGTPVVRLAPIARQRVERAAQAVQDLLARGVVAYGITTGFGAFKDRV 72 L IE VLA+A Q + + R+R+ + A+ + LL + V YG+TTG+G Sbjct: 16 LRIEDVLALANRQAPVQLQNDSEY-RERIAKGARFLDSLLDKEGVIYGVTTGYGDSCVVA 74 Query: 73 IAPDQVERLQYNILVSHAVGVGPVFDIPTTRAIMLIRANTLARGHSGVRLQTVERLLDML 132 + VE L ++ H G+G + D TRA++ R +L G SGVR++ +ERL L Sbjct: 75 VPLHHVEALPRHLYTFHGCGLGKLLDAQATRAVLAARLQSLCHGVSGVRIELLERLHAFL 134 Query: 133 NQGIHPRIPCKGSLGASGDLAPLAHMALPLIGLGEVEWQGEVLPAATALERLGWQPLHLA 192 I P IP +GS+GASGDL PL+++A L G EV ++GE AA LGW+PL L Sbjct: 135 EHDILPLIPEEGSVGASGDLTPLSYVAATLSGEREVLFKGERRQAADVHRELGWEPLVLR 194 Query: 193 AKEGLALTNGTAVMCALGVIETARAETLSATADIAGCLSLEALYGTPAAFDARLHALRPF 252 KE LAL NGTAVM L + ARA+ L A L++ AL G P FD RL A +P Sbjct: 195 PKEALALMNGTAVMTGLACLAYARADYLLQLATRITALNVVALQGNPEHFDERLFATKPH 254 Query: 253 PRQIECAAHLRRLLAGSTFVRNNDPRH-VQDAYTLRCIPQVHGAVRDAIAYARWVFAIEL 311 P Q++ AA LR+ LA P H +QD Y+LRC P V G + D++ + R IEL Sbjct: 255 PGQMQVAAWLRKDLA---IDAPTAPLHRLQDRYSLRCAPHVLGVLADSLNWLRSFIEIEL 311 Query: 312 NAVTDNPLLFVDDDGNVEVISGGNFHGEPLAIALDYLGLAVAELGNIAERRLMRLTDEAS 371 N+ DNP++ + + V+ GG+F+G +A A+D L VA + ++ +R+L L DE Sbjct: 312 NSANDNPIIDAEAE---RVLHGGHFYGGHIAFAMDSLKNLVANVADLLDRQLALLVDERY 368 Query: 372 NTHVLPAFLTRAGG----LNSGFMIVQYTAAALATENKVLAHPASVDSIPTSANVEDHVS 427 N H LP+ L+ A LN GF VQ +A E PASV S T + +D VS Sbjct: 369 N-HGLPSNLSGASAERAMLNHGFKAVQIGTSAWTAEALKNTMPASVFSRSTECHNQDKVS 427 Query: 428 MGVTAGLKLRSIIDNVSQILALELFAAAQGIDFRRQELGSQARLGRGTGPVY-----ELI 482 MG A +++ Q+ A L AA QG+ R SQA R P EL Sbjct: 428 MGTIAARDAIRVLELTEQVAAATLLAANQGVWLR-----SQAEDARPLPPALAAMHAELA 482 Query: 483 RQYVPFIAEDTLLHPYITIISELVAQ 508 + + P I ED L + + + +A+ Sbjct: 483 KDFAPVI-EDRALEGELRLCLQRIAE 507 Lambda K H 0.322 0.137 0.396 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: 614 Number of extensions: 27 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: 523 Length of database: 514 Length adjustment: 35 Effective length of query: 488 Effective length of database: 479 Effective search space: 233752 Effective search space used: 233752 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: 52 (24.6 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