Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate GFF3628 Psest_3695 Histidine ammonia-lyase
Query= curated2:A9WHT8 (523 letters) >FitnessBrowser__psRCH2:GFF3628 Length = 510 Score = 263 bits (671), Expect = 1e-74 Identities = 186/497 (37%), Positives = 260/497 (52%), Gaps = 16/497 (3%) Query: 5 EVILDGESLT-IEQVLAVAYGQPGTPVVRLAPIA-RQRVERAAQAVQDLLARGVVAYGIT 62 E ++ GE+L IE VLAVA Q P A A R R+ R AQ + LL R V YG+T Sbjct: 3 EPVIFGENLLRIEDVLAVA--QRRAPARLQADEAFRSRIARGAQFLDTLLDREGVIYGVT 60 Query: 63 TGFGAFKDRVIAPDQVERLQYNILVSHAVGVGPVFDIPTTRAIMLIRANTLARGHSGVRL 122 TG+G + QVE L ++ H G+G + + TRA++ R +L G SGVR+ Sbjct: 61 TGYGDSCVVAVPLHQVEALPQHLFTFHGCGLGKLLEAEATRAVLAARLRSLTHGMSGVRI 120 Query: 123 QTVERLLDMLNQGIHPRIPCKGSLGASGDLAPLAHMALPLIGLGEVEWQGEVLPAATALE 182 + +ER+ L + P IP +GS+GASGDL PL+++A L G EV ++GE AA Sbjct: 121 ELLERMQAFLEHDVLPLIPEEGSVGASGDLTPLSYVAAALAGEREVLYRGERRSAAEVHR 180 Query: 183 RLGWQPLHLAAKEGLALTNGTAVMCALGVIETARAETLSATADIAGCLSLEALYGTPAAF 242 +LGW PL L KE LAL NGTAVM L + ARA+ L A L++ AL G P F Sbjct: 181 QLGWTPLTLRPKEALALMNGTAVMTGLACLAYARADYLLQLATRITALNVIALQGNPEHF 240 Query: 243 DARLHALRPFPRQIECAAHLRRLLAGSTFVRNNDPRH-VQDAYTLRCIPQVHGAVRDAIA 301 D RL A +P P Q + AA +R+ LA P H +QD Y++RC P V G + D++ Sbjct: 241 DERLFAAKPHPGQTQVAAWIRQDLAIDAPAA---PLHRLQDRYSIRCAPHVLGVLADSLG 297 Query: 302 YARWVFAIELNAVTDNPLLFVDDDGNVEVISGGNFHGEPLAIALDYLGLAVAELGNIAER 361 R ELN+ DNP++ D N V+ GG+F+G +A A+D L VA + ++ +R Sbjct: 298 LLRQFIETELNSANDNPII---DADNERVLHGGHFYGGHIAFAMDSLKNLVANVADLLDR 354 Query: 362 RLMRLTDEASNTHVLPAFLTRAGG----LNSGFMIVQYTAAALATENKVLAHPASVDSIP 417 +L L D N H LP+ L+ A +N GF VQ +A E + PASV S Sbjct: 355 QLALLVDTRYN-HGLPSNLSGAPAATAMINHGFKAVQIGTSAWTAEALKNSMPASVFSRS 413 Query: 418 TSANVEDHVSMGVTAGLKLRSIIDNVSQILALELFAAAQGIDFRRQELGSQARLGRGTGP 477 T + +D VSMG A ++ Q+ A L AA QG+ R+++ ++ Sbjct: 414 TECHNQDKVSMGTIAARDALRSLELSEQVAAATLLAAQQGVWLRQRQEDARPLPAPLAAM 473 Query: 478 VYELIRQYVPFIAEDTL 494 EL + P I + L Sbjct: 474 HSELAETFPPLIEDRAL 490 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: 619 Number of extensions: 26 Number of successful extensions: 5 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: 510 Length adjustment: 35 Effective length of query: 488 Effective length of database: 475 Effective search space: 231800 Effective search space used: 231800 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