Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate GFF409 PS417_02080 histidine ammonia-lyase
Query= curated2:Q1IRT8 (516 letters) >FitnessBrowser__WCS417:GFF409 Length = 513 Score = 272 bits (696), Expect = 2e-77 Identities = 176/497 (35%), Positives = 265/497 (53%), Gaps = 25/497 (5%) Query: 11 LTLDEVREVVYEQRPVLLDSDA--RAAVDRARAVIEDVVANDRLAYAVTTGVGKLSDVRI 68 L +++V + Q P L SDA R + + ++ ++ + + Y VTTG G V + Sbjct: 15 LRIEDVLALANRQAPTQLQSDAAYRQRIAKGAQFLDSLLDKEGVIYGVTTGYGDSCVVAV 74 Query: 69 PPAENRTLQLNLMRSHAVGVGDPLSEQVSRAMMLLRANSLCKGWSGVRGLVIDTLCEMLN 128 P L +L H G+G L Q +RA++ R SLC G SGVR +++ L L Sbjct: 75 PLQHVEALPRHLYTFHGCGLGKLLDAQATRAVLAARLQSLCHGVSGVRVELLERLHAFLE 134 Query: 129 RGVHPVIPSQGSVGASGDLAPLAHQGLVLIGEGEAFYQGKRVSGAEALRAAGIKPITLEA 188 V P+IP +GSVGASGDL PL++ L GE E ++G+R + R G +P+ L Sbjct: 135 HDVLPLIPEEGSVGASGDLTPLSYVAATLSGEREVMFRGERRQAIDVHRELGWEPLVLRP 194 Query: 189 KETISLINGTQAMLAVGLLAVLDAEILAETADAVGALALDVLQGTDAAFDERIHKARPHS 248 KE ++L+NGT M + LA A+ L + A + AL + LQG FDER+ A+PH Sbjct: 195 KEALALMNGTAVMTGLACLAFARADYLLQLATRITALNVVALQGNPEHFDERLFAAKPHP 254 Query: 249 GQIQVAANLRRLLAGSQIHESHKDCARVQDAYSLRCMPQVHGAVRDTIHYCRSVFEVEMN 308 GQ+QVAA LR+ LA I R+QD YSLRC P V G + D++++ RS E+E+N Sbjct: 255 GQMQVAAWLRKDLA---IDAPTAPLHRLQDRYSLRCAPHVLGVLADSLNWLRSFIEIELN 311 Query: 309 SAVDNPLVFPEPKKVGERSDAPVHGDIISGGNFHGEPVAFALDFLAIALSALAGISERRI 368 SA DNP++ E ++V + GG+F+G +AFA+D L ++ +A + +R++ Sbjct: 312 SANDNPIIDAEEERV------------LHGGHFYGGHIAFAMDSLKTLVANVADLLDRQL 359 Query: 369 ERLVNPALSEGLPAFL----APGAGLNSGFMMPQVTAAALVSENKVLSHPASVDSITTSG 424 LV+ + GLP+ L A A +N GF Q+ +A +E + PASV S +T Sbjct: 360 ALLVDVRYNHGLPSNLSGAPADRAMINHGFKAVQIGTSAWTAEALKNTMPASVFSRSTEC 419 Query: 425 NKEDFVSMGMTAALKLQRIVQNTRNVMAIEALAAAQALDFKAPLKTTK----LLQKVHAA 480 + +D VSMG AA R+++ T V A LAA Q + +A + + L +H A Sbjct: 420 HNQDKVSMGTIAARDAIRVLELTEQVAAATLLAANQGVWLRAQAEDARPLPPALAAMHEA 479 Query: 481 VRAVSPQITEDRILTAD 497 + P + EDR L + Sbjct: 480 LAKDFPPVIEDRALEGE 496 Lambda K H 0.318 0.132 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: 568 Number of extensions: 22 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: 516 Length of database: 513 Length adjustment: 35 Effective length of query: 481 Effective length of database: 478 Effective search space: 229918 Effective search space used: 229918 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 (21.7 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