Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate AO356_09175 AO356_09175 histidine ammonia-lyase
Query= curated2:A9WHT8 (523 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09175 Length = 514 Score = 267 bits (682), Expect = 8e-76 Identities = 194/519 (37%), Positives = 269/519 (51%), Gaps = 25/519 (4%) Query: 1 MQIREVILDGES-LTIEQVLAVAYGQPGTPVVRLAPIARQRVERAAQAVQDLLARGVVAY 59 M E + GE L IE VLA+A Q T + + P RQR+ + AQ + LL + V Y Sbjct: 3 MPTLEPVTFGERPLRIEDVLALANRQAPTQL-QDDPAFRQRIAKGAQFLDSLLDKEGVIY 61 Query: 60 GITTGFGAFKDRVIAPDQVERLQYNILVSHAVGVGPVFDIPTTRAIMLIRANTLARGHSG 119 G+TTG+G + VE L ++ H G+G + D TRA++ R +L G SG Sbjct: 62 GVTTGYGDSCVVAVPLHHVEALPRHLYTFHGCGLGKLLDAQATRAVLAARLQSLCHGVSG 121 Query: 120 VRLQTVERLLDMLNQGIHPRIPCKGSLGASGDLAPLAHMALPLIGLGEVEWQGEVLPAAT 179 VR++ +ERL L I P IP +GS+GASGDL PL+++A L G EV ++GE AA Sbjct: 122 VRVELLERLQAFLEHDILPLIPEEGSVGASGDLTPLSYVAATLSGEREVMFRGERRLAAD 181 Query: 180 ALERLGWQPLHLAAKEGLALTNGTAVMCALGVIETARAETLSATADIAGCLSLEALYGTP 239 LGW PL L KE LAL NGTAVM L + ARA+ L A L++ AL G P Sbjct: 182 VHRELGWTPLVLRPKEALALMNGTAVMTGLACLAFARADYLLQLATRITALNVVALQGNP 241 Query: 240 AAFDARLHALRPFPRQIECAAHLRRLLAGSTFVRNNDPRH-VQDAYTLRCIPQVHGAVRD 298 FD RL A +P P Q++ AA LR+ LA P H +QD Y+LRC P V G + D Sbjct: 242 EHFDERLFAAKPHPGQMQVAAWLRKDLA---IDAPTAPLHRLQDRYSLRCAPHVLGVLAD 298 Query: 299 AIAYARWVFAIELNAVTDNPLLFVDDDGNVEVISGGNFHGEPLAIALDYLGLAVAELGNI 358 ++ + R ELN+ DNP++ + + V+ GG+F+G +A A+D L VA + ++ Sbjct: 299 SLGWLRSFIETELNSANDNPIIDAEAE---RVLHGGHFYGGHIAFAMDSLKNLVANVADL 355 Query: 359 AERRLMRLTDEASNTHVLPAFLTRAGG----LNSGFMIVQYTAAALATENKVLAHPASVD 414 +R+L L DE N H LP+ L+ A LN GF VQ +A E PASV Sbjct: 356 LDRQLALLVDERYN-HGLPSNLSGASAERAMLNHGFKAVQIGTSAWTAEALKNTMPASVF 414 Query: 415 SIPTSANVEDHVSMGVTAGLKLRSIIDNVSQILALELFAAAQGIDFRRQELGSQARLGRG 474 S T + +D VSMG A +++ Q+ A L AA QG+ R S+A R Sbjct: 415 SRSTECHNQDKVSMGTIAARDAIRVLELTEQVAAATLLAANQGVWLR-----SRAEDARP 469 Query: 475 TGPV-----YELIRQYVPFIAEDTLLHPYITIISELVAQ 508 P +L + P I ED L + + + +A+ Sbjct: 470 LPPALAAMHQQLAEDFAPVI-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: 602 Number of extensions: 25 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