Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate RR42_RS01710 RR42_RS01710 tyrosine ammonia-lyase
Query= curated2:Q67JH4 (507 letters) >FitnessBrowser__Cup4G11:RR42_RS01710 Length = 532 Score = 373 bits (958), Expect = e-108 Identities = 228/523 (43%), Positives = 311/523 (59%), Gaps = 25/523 (4%) Query: 3 AVEL-GAHLTLPEVVAVARHGARVVLTPEVRQRVARASEMVERLVRERRPVYGITTGFGK 61 AVE+ G LT + VA+ L R VA A E L P+YG++TGFG+ Sbjct: 5 AVEVDGQQLTAAALAQVAQGRRPASLDQAARAHVADARARFEELASSNIPIYGVSTGFGE 64 Query: 62 FSDVPISAEQTEALQRNLLMSHACAVGEPLAAEVVRAMLLLRAQALSRGHSGIRAETLEM 121 + E ALQ NLL SH VG E VRAM++ RA AL+RG+S +R +E Sbjct: 65 LVHNWVDIEHAGALQENLLRSHCAGVGPLFGREEVRAMMVARANALARGYSAVRPLVIEQ 124 Query: 122 LVAFLNLGLTPVVPEQGSLGASGDLAPLAHMSLPLIGLGEAVV-NGERLSGAEALQRVGL 180 L+ ++ G+TP VP+ GSLGASGDLAPL+H+++ LIG G+ ++ +G + L+ G+ Sbjct: 125 LLRYVEAGITPAVPQVGSLGASGDLAPLSHIAITLIGEGKVLLADGTTAPTGQVLREHGI 184 Query: 181 RPLTLTAKEGLALINGTQAMTALGSLGLHDAQVLLKTADIAAAMTAEALGAIPAAWDPRV 240 P+ L+ KEGLALINGT AMT + L L + + A+I AA+ E L A A+ Sbjct: 185 EPIKLSHKEGLALINGTSAMTGMACLLLETMRAQVTQAEIIAALALEGLNASADAFMTHG 244 Query: 241 QAL-RLHTGQQAAARNLRRLTEGS-RLTTR---PGQMRT--------------QDPYTLR 281 + + H GQ +A NLR L GS RL+ G+M+T Q YTLR Sbjct: 245 HDIAKPHPGQVQSAANLRALLAGSTRLSGHGQLAGEMKTRAGDEKNTGTGVFIQKAYTLR 304 Query: 282 CLPQVHGASRTAIEHVAQVLDWEMNAVTDNPLLFPDDDEVISGGNFHGQPVALALDYLAI 341 C+PQV GA R + H A V++ E+N+ DNPL F DD E+ GGNFHGQ VA A+D+LAI Sbjct: 305 CIPQVLGAVRDTLGHCATVVERELNSSNDNPLFF-DDGELFHGGNFHGQQVAFAMDFLAI 363 Query: 342 AVAELGDIAERRIERLVNPQL-SGLPAFL-TRNGGVHSGLMITQYTAASLVSENKVLAHP 399 A +LG ++ERR+ RL++P L +GLPAFL N G+ G QY A +L++EN+ + P Sbjct: 364 AATQLGVVSERRLNRLLSPHLNNGLPAFLAAANEGLSCGFAGAQYPATALIAENRTICSP 423 Query: 400 ASVDSIPSSANQEDHVSMGTTAARKARQVIANVRRVLAIELLCAAQALEFVGP-ERLAPA 458 AS+ S+PS+ + +D VSMG AR AR++I N + +LA+ELL A QA E G E L+PA Sbjct: 424 ASIQSVPSNGDNQDVVSMGLIGARNARRIIDNNQYILAVELLAACQAAELAGAVESLSPA 483 Query: 459 TRAAYAAIRERVAPLSGDRVLAPDIEALAELVHNGELVAAVEA 501 RA +A +RERV L+ DR + DIEA+A + G LV V A Sbjct: 484 GRAVFAFVRERVPFLAMDRYMTDDIEAIAAQLRAGALVGVVRA 526 Lambda K H 0.318 0.132 0.370 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: 663 Number of extensions: 39 Number of successful extensions: 6 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: 507 Length of database: 532 Length adjustment: 35 Effective length of query: 472 Effective length of database: 497 Effective search space: 234584 Effective search space used: 234584 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