Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 5211101 Shew_3517 histidine ammonia-lyase (RefSeq)
Query= BRENDA::P42357 (657 letters) >FitnessBrowser__PV4:5211101 Length = 520 Score = 283 bits (723), Expect = 2e-80 Identities = 177/482 (36%), Positives = 264/482 (54%), Gaps = 20/482 (4%) Query: 114 IELDGDRLTTEDLVNLGKG-RYKIKLTPTAEKRVQKSREVIDSIIKEKTVVYGITTGFGK 172 +E L E++V + KG + ++K + ++ +QK IDS++ E+ VVYG+TTG+G Sbjct: 14 VEFGQRNLNLEEVVAIAKGAKAQLKESADYQEYIQKGARFIDSLLAEEGVVYGVTTGYGD 73 Query: 173 FARTVIPINKLQELQVNLVRSHSSGVGKPLSPERCRMLLALRINVLAKGYSGISLETLKQ 232 + ++ + EL ++L R H G+G LS + R ++A R++ LA G SG+S E LK+ Sbjct: 74 SCTVTVGLDLVHELPLHLSRFHGCGMGNILSVMQARAVMACRLSSLAVGKSGVSYELLKR 133 Query: 233 VIEMFNASCLPYVPEKGTVGASGDLAPLSHLALGLVGEGKMWSPKSGWADAKYVLEAHGL 292 + + N P +PE+G+VGASGDL PLS+LA LVGE ++ A A E + Sbjct: 134 IETLLNLGITPVIPEEGSVGASGDLTPLSYLAAVLVGEREVIYQGERRATADVYREL-DI 192 Query: 293 KPVILKPKEGLALINGTQMITSLGCEAVERASAIARQADIVAALTLEVLKGTTKAFDTDI 352 P+ L+PKEGLAL+NGT ++T+L C A +RA + R A + A+ LKG + FD + Sbjct: 193 TPLTLRPKEGLALMNGTAVMTALACLAYDRAQYLNRLASRITAMASLTLKGNSNHFDDIL 252 Query: 353 HALRPHRGQIEVAFRFRSLLDSDHHPSEIAESHRFCDRVQDAYTLRCCPQVHGVVNDTIA 412 A +PH GQ ++A R L+ HP R DR+QD Y++RC P + GV+ D + Sbjct: 253 FAAKPHPGQNQIAAWIREDLNHHEHP-------RNSDRLQDRYSIRCAPHIIGVLQDALP 305 Query: 413 FVKNIITTELNSATDNPMVFANRGETVSGGNFHGEYPAKALDYLAIGIHELAAISERRIE 472 F++ I TELNSA DNP+V + GG+F+G + +D + I +A + +R++ Sbjct: 306 FMRQFIETELNSANDNPIVDGEGEHVLHGGHFYGGHIGFVMDSMKNAIANIADLIDRQMA 365 Query: 473 RLCNPSLSE-LPAFLVAEGG----LNSGFMIAHCTAAALVSENKALCHPSSVDSLSTSAA 527 + +P + LPA L G +N GF +A +E P+SV S ST Sbjct: 366 LVMDPKFNNGLPANLSGAQGSRKAINHGFKAVQIGVSAWTAEALKNTMPASVFSRSTECH 425 Query: 528 TEDHVSMGGWAARKALRVIEHVEQVLAIELLAACQGIEF------LRPLKTTTPLEKVYD 581 +D VSMG AAR +RV++ EQV A LLA QGI L TT + K D Sbjct: 426 NQDKVSMGTIAARDCMRVLQLTEQVAAAALLAMTQGIHLRIAQGELCHASLTTSVAKTLD 485 Query: 582 LV 583 V Sbjct: 486 QV 487 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: 719 Number of extensions: 34 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: 520 Length adjustment: 37 Effective length of query: 620 Effective length of database: 483 Effective search space: 299460 Effective search space used: 299460 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 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