Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate WP_090440762.1 BLS63_RS05225 aromatic amino acid lyase
Query= curated2:Q67JH4 (507 letters) >NCBI__GCF_900100495.1:WP_090440762.1 Length = 513 Score = 265 bits (676), Expect = 4e-75 Identities = 177/488 (36%), Positives = 267/488 (54%), Gaps = 20/488 (4%) Query: 10 LTLPEVVAVARHGARVVLT--PEVRQRVARASEMVERLVRERRPVYGITTGFGKFSDVPI 67 LT+ +VV +A+ AR +L P R+++A+ + ++ L+ + +YG+TTG+G V + Sbjct: 16 LTIEQVVGLAQRRARALLQDDPGYREKIAKGARFLDSLLDQEGVIYGVTTGYGDSCVVAV 75 Query: 68 SAEQTEALQRNLLMSHACAVGEPLAAEVVRAMLLLRAQALSRGHSGIRAETLEMLVAFLN 127 Q EAL R+L H C +G+ L RA+L R Q+L +G SG+R E LE L AFL+ Sbjct: 76 PLHQVEALPRHLYTFHGCGLGKLLDPASTRAVLAARLQSLCQGVSGVRVELLERLQAFLD 135 Query: 128 LGLTPVVPEQGSLGASGDLAPLAHMSLPLIGLGEAVVNGERLSGAEALQRVGLRPLTLTA 187 + P++PE+GS+GASGDL PL++++ L G E + GER S AE +G PL L Sbjct: 136 FDVLPLIPEEGSVGASGDLTPLSYVAASLSGEREVLYQGERRSAAEVHAELGWTPLLLRP 195 Query: 188 KEGLALINGTQAMTALGSLGLHDAQVLLKTADIAAAMTAEALGAIPAAWDPRVQALRLHT 247 KE LAL+NGT MTAL L A+ LLK A A+ AL P +D R+ A + H Sbjct: 196 KEALALMNGTAVMTALACLAFSRAEYLLKLATRITALNVVALQGNPEHFDERLFAAKPHP 255 Query: 248 GQQAAARNLRRLTEGSRLTTRPGQM-RTQDPYTLRCLPQVHGASRTAIEHVAQVLDWEMN 306 GQ A LR E + + R QD Y+LRC P V G ++ + Q ++ E+N Sbjct: 256 GQLQVAAWLR---EDLAIDAPTAPLHRLQDRYSLRCAPHVLGVLADSLGLLRQFIEIELN 312 Query: 307 AVTDNPLLFPDDDEVISGGNFHGQPVALALDYLAIAVAELGDIAERRIERLVNPQLS-GL 365 + DNPL+ + V+ GG+F+G +A A+D L VA + D+ +R++ LV+ + + GL Sbjct: 313 SANDNPLIDAEAGRVLHGGHFYGGHIAFAMDSLKNLVANVADLLDRQLALLVDQRYNHGL 372 Query: 366 PAFLT----RNGGVHSGLMITQYTAASLVSENKVLAHPASVDSIPSSANQEDHVSMGTTA 421 P+ L+ + ++ G Q A++ +E PAS+ S + + +D VSMGT A Sbjct: 373 PSNLSGAPAASAMINHGFKAVQIGASAWTAEALKNGMPASLFSRSTECHNQDKVSMGTIA 432 Query: 422 ARKARQVIANVRRVLAIELLCAAQA--LEFVGPERLAPATRAAYAAIRERVA----PLSG 475 AR A + + +V A LL A Q L ++ P A AA+RE++A PL Sbjct: 433 ARDALRSLELSEQVAAATLLAANQGVWLRLRDGQQSVP---APLAAMREQLAADFPPLLE 489 Query: 476 DRVLAPDI 483 DR L ++ Sbjct: 490 DRALEGEL 497 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: 582 Number of extensions: 27 Number of successful extensions: 3 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: 513 Length adjustment: 34 Effective length of query: 473 Effective length of database: 479 Effective search space: 226567 Effective search space used: 226567 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 24 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