Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate WP_057507134.1 ABB28_RS02670 aromatic amino acid lyase
Query= BRENDA::P42357 (657 letters) >NCBI__GCF_001431535.1:WP_057507134.1 Length = 516 Score = 276 bits (705), Expect = 2e-78 Identities = 179/463 (38%), Positives = 256/463 (55%), Gaps = 15/463 (3%) Query: 109 EPEKYIELDGDRLTTEDLVNLGKGRYKIKL--TPTAEKRVQKSREVIDSIIKEKTVVYGI 166 EP LT ED+V L R + L P R+Q+ + +D +++E VVYG+ Sbjct: 4 EPLPSCRFGAGPLTIEDVVALADRRAQAVLDDAPGFRARIQRGADFLDRLLREDGVVYGV 63 Query: 167 TTGFGKFARTVIPINKLQELQVNLVRSHSSGVGKPLSPERCRMLLALRINVLAKGYSGIS 226 TTG+G TVIP + + EL +L H G+G+ L + R +LA R+ L++G SG S Sbjct: 64 TTGYGDSCTTVIPPSLVAELPHHLYTYHGCGLGRFLDAQETRAVLAARLASLSQGMSGTS 123 Query: 227 LETLKQVIEMFNASCLPYVPEKGTVGASGDLAPLSHLALGLVGEGKMWSPKSGWADAKYV 286 + L+ + + LP +P +G+VGASGDL PLS++A L GE ++ S + A+ V Sbjct: 124 VALLEGLAALLQHDVLPRIPAEGSVGASGDLTPLSYVAAVLCGEREVLFEGSVQSAAE-V 182 Query: 287 LEAHGLKPVILKPKEGLALINGTQMITSLGCEAVERASAIARQADIVAALTLEVLKGTTK 346 L GL+P+ L+PKEGLAL+NGT ++T L C A RA + R A + A + G Sbjct: 183 LPRIGLQPLRLRPKEGLALMNGTAVMTGLACLAWHRADYLCRLATRLTAFNVLASDGNAH 242 Query: 347 AFDTDIHALRPHRGQIEVAFRFRSLLDSDHHPSEIAESHRFCDRVQDAYTLRCCPQVHGV 406 FD + A +PH GQ +A R R+ L SD P R R+QD Y+LRC P V GV Sbjct: 243 HFDETLFAAKPHPGQARIAARLRADLHSDRPP-------RNEQRLQDRYSLRCAPHVIGV 295 Query: 407 VNDTIAFVKNIITTELNSATDNPMVFANRGETVSGGNFHGEYPAKALDYLAIGIHELAAI 466 + DT+ F++ +I TELNSA DNP++ + + GG+F+G + A A+D L + LA + Sbjct: 296 LEDTLPFLRQLIETELNSANDNPLIDPDEERVLHGGHFYGGHIALAMDTLKNTVANLADL 355 Query: 467 SERRIERLCNPSLSE-LPAFLVAEGG----LNSGFMIAHCTAAALVSENKALCHPSSVDS 521 +R++ L + S LPA L A G +N G + +A +E P+SV S Sbjct: 356 LDRQLALLVDARYSHGLPANLSAATGPRAAINHGLKALQISVSAWTAEALKNTLPASVFS 415 Query: 522 LSTSAATEDHVSMGGWAARKALRVIEHVEQVLAIELLAACQGI 564 ST +D VSMG AAR LRVIE EQV+A L+AA Q + Sbjct: 416 RSTECHNQDKVSMGTIAARDCLRVIELAEQVVAGMLIAARQAV 458 Lambda K H 0.319 0.135 0.398 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: 726 Number of extensions: 36 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: 657 Length of database: 516 Length adjustment: 36 Effective length of query: 621 Effective length of database: 480 Effective search space: 298080 Effective search space used: 298080 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 (21.7 bits) S2: 53 (25.0 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