Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate HSERO_RS22680 HSERO_RS22680 histidine ammonia-lyase
Query= curated2:A8MF64 (507 letters) >FitnessBrowser__HerbieS:HSERO_RS22680 Length = 542 Score = 372 bits (954), Expect = e-107 Identities = 212/538 (39%), Positives = 314/538 (58%), Gaps = 34/538 (6%) Query: 1 MKKIMIDGEQLTLQDIIHVTRNFY-EIELSEDAKNRVRNNRKVVDR--YVEEEKVVYGIT 57 M I IDG LT ++ V R + ++ L++ ++ ++ +R ++ +E ++Y Sbjct: 1 MSTITIDGFNLTAAQVVSVARAPHLKVALADSSRAALKQSRDYIESTWMHDEAPMMYSFN 60 Query: 58 TGFGKFSDVVISKSETEALQRNLIISHACGVGNPLEEDVVRGIMLLRANALSKGYSGIRL 117 TG G D I E Q LI +H+ G+G E+V R MLLRANA + YS R+ Sbjct: 61 TGVGLLKDTRIKVEHIELFQTQLIRAHSAGIGEAFSEEVSRATMLLRANAFASNYSAPRV 120 Query: 118 ETLSTLIEMLNKGVHPVIPEKGSLGASGDLAPLSHMVLVLIG--EGEAIYQGKRMSGREA 175 E + L+ +N G+HP++P+KGS+GASGDLAPL+++ + G E E +YQG+RM EA Sbjct: 121 EVVDRLLAFINAGIHPIMPQKGSVGASGDLAPLAYLAAAIAGFDEAEVMYQGQRMRATEA 180 Query: 176 MEAAGIRPVV--LTSKEGLALINGTQVMTAIGALTVYDAINLSKISDIAAALTIEAQRGI 233 +E AGI PV L +K+ ALING A+ L +DA +L + ++ LT+EA R Sbjct: 181 IEQAGIGPVKFDLKAKDASALINGCTASLAVAILAAHDARHLLTDACLSLGLTLEAMRAE 240 Query: 234 VTAFDKRVHEVRPHAGQISCAENLNRLLEGSTYTTKQGE----------------IKVQD 277 ++AFD R+ + RPHAGQI AE + LL+GST TT ++QD Sbjct: 241 MSAFDPRIQQARPHAGQIKTAEVIRTLLQGSTRTTHAARAVQLPDELRRTDIAYTARIQD 300 Query: 278 AYTLRCIPQIHGASKDAIQYVENKINIEINSATDNPLIFSEDN----DVISGGNFHGQPM 333 Y+LRC PQ++G DA+ Y++ I E NSATDNPLIF ++ ++ISGGNFHGQ + Sbjct: 301 VYSLRCAPQVYGPVFDALDYIDTIIEKETNSATDNPLIFHKEEGEGFEIISGGNFHGQYL 360 Query: 334 ALSFDFLGIALAEIANVSERRIERLVNPQLS-GLPA-FLTEKGGLNSGFMITQYSAAALV 391 A + D L +A+ ++ ++ ERRI RL++P LS GLP ++ G+N+G+ + Q S ++LV Sbjct: 361 AQAMDLLAMAITDLGSICERRIARLIDPTLSWGLPRNLMSGVRGVNTGYPVVQCSMSSLV 420 Query: 392 SENKVLAHPASVDSIPSSANQEDHVSMGTIAARKAREIYKNAVNVVAIELMAAAQGIDFY 451 EN+ L P SVDSIPS N EDH+S T ARKA + +N +V +E++ AAQ + Sbjct: 421 MENRTLCMPGSVDSIPSKGNSEDHISNSTWCARKAMTVVQNTQYIVGVEMLLAAQALTMT 480 Query: 452 EG----YTLGEGTQIAYDTIRNKV-SKLQEDRVMYFDINQCANLIFSGELIEAVEKAV 504 E + LG+GTQ AY IR ++ + L DR + D+ + SG + AV A+ Sbjct: 481 EALLKDFVLGQGTQAAYAEIRRQIPACLDGDRWFHDDVQAAHGFVVSGSVRNAVLAAI 538 Lambda K H 0.316 0.133 0.364 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: 575 Number of extensions: 23 Number of successful extensions: 7 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: 542 Length adjustment: 35 Effective length of query: 472 Effective length of database: 507 Effective search space: 239304 Effective search space used: 239304 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 (21.6 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