Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 203452 SO4374 histidine ammonia-lyase, putative (NCBI ptt file)
Query= BRENDA::P42357 (657 letters) >FitnessBrowser__MR1:203452 Length = 521 Score = 294 bits (753), Expect = 6e-84 Identities = 188/497 (37%), Positives = 277/497 (55%), Gaps = 22/497 (4%) Query: 111 EKYIELDGDRLTTEDLVNLGKGRYKIKLTPTAEKR--VQKSREVIDSIIKEKTVVYGITT 168 E IE LT E +V + KG K+KL A+ + +QK IDS++ E+ VVYG+TT Sbjct: 12 ESPIEFGRQLLTLEQVVAVAKGA-KVKLCDDADYQEYIQKGARFIDSLLHEEGVVYGVTT 70 Query: 169 GFGKFARTVIPINKLQELQVNLVRSHSSGVGKPLSPERCRMLLALRINVLAKGYSGISLE 228 G+G + ++ + EL ++L R H G+G+ LS + R ++A R+N LA G SG++ E Sbjct: 71 GYGDSCTVNVSLDLVHELPLHLSRFHGCGLGEVLSVMQARAVMACRLNSLAIGKSGVTYE 130 Query: 229 TLKQVIEMFNASCLPYVPEKGTVGASGDLAPLSHLALGLVGEGKMWSPKSGWADAKYVLE 288 LK++ + N + +P +PE+G+VGASGDL PLS+LA LVGE ++ A K V Sbjct: 131 LLKRIQTLLNLNIVPVIPEEGSVGASGDLTPLSYLAAVLVGEREVIYQGERRA-TKEVYH 189 Query: 289 AHGLKPVILKPKEGLALINGTQMITSLGCEAVERASAIARQADIVAALTLEVLKGTTKAF 348 + P +L+PKEGLAL+NGT ++T+L C A +RA +AR A + A+ LKG + F Sbjct: 190 ELNITPHVLRPKEGLALMNGTAVMTALACLAFDRAQYLARLASRITAMASLTLKGNSNHF 249 Query: 349 DTDIHALRPHRGQIEVAFRFRSLLDSDHHPSEIAESHRFCDRVQDAYTLRCCPQVHGVVN 408 D + A +PH GQ ++A R L+ HP R DR+QD Y++RC P + GV+ Sbjct: 250 DDILFAAKPHPGQNQIATWIREDLNHHVHP-------RNSDRLQDRYSIRCAPHIIGVLQ 302 Query: 409 DTIAFVKNIITTELNSATDNPMVFANRGETVSGGNFHGEYPAKALDYLAIGIHELAAISE 468 D + F++ I TE+NSA DNP+V A + GG+F+G + A A+D L + +A + + Sbjct: 303 DALPFMRQFIETEVNSANDNPIVDAEGEHILHGGHFYGGHIAFAMDSLKNIVANIADLID 362 Query: 469 RRIERLCNPSLSE-LPAFLVAEGG----LNSGFMIAHCTAAALVSENKALCHPSSVDSLS 523 R++ + +P + LPA L G +N GF +A +E P+SV S S Sbjct: 363 RQMALVMDPKFNNGLPANLSGSTGPRRAINHGFKAVQIGVSAWTAEALKHTMPASVFSRS 422 Query: 524 TSAATEDHVSMGGWAARKALRVIEHVEQVLAIELLAACQGIEF------LRPLKTTTPLE 577 T +D VSMG AAR +RV++ EQV A LLA QGI+ L T L Sbjct: 423 TECHNQDKVSMGTIAARDCMRVLQLTEQVAAAALLAMTQGIDLRITQNELDEASLTPSLA 482 Query: 578 KVYDLVRSVVRPWIKDR 594 VR+ P ++DR Sbjct: 483 TTLAQVRADFEPLVEDR 499 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: 720 Number of extensions: 31 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: 521 Length adjustment: 37 Effective length of query: 620 Effective length of database: 484 Effective search space: 300080 Effective search space used: 300080 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