Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate N515DRAFT_2941 N515DRAFT_2941 histidine ammonia-lyase
Query= curated2:Q7NCB3 (514 letters) >FitnessBrowser__Dyella79:N515DRAFT_2941 Length = 629 Score = 364 bits (934), Expect = e-105 Identities = 233/525 (44%), Positives = 294/525 (56%), Gaps = 77/525 (14%) Query: 10 LDGCSLAVDDLVAVARGGVPVRLSPASLELVRRSRAFVEALLEGDEIVYGITTGFGYFKN 69 LDG SL LVA AR VPV L A L V+R+ F+ + E YG+TTGFG + Sbjct: 8 LDGSSLTRAQLVAAARQRVPVALDEAQLARVQRAADFLADKVSCGEPTYGVTTGFGSNAD 67 Query: 70 RRIPR-----------------SAVEQLQQNLLMSSAAGLGEPFGREVVRAMLLLRANTL 112 + + + +E+LQ NL+ + A +G+PF +VVRAML++R NTL Sbjct: 68 KLLGAHRLRDELPGGHPEKPEGTLLEELQHNLITTHAVCVGKPFAEDVVRAMLVIRINTL 127 Query: 113 AQGYSGVRPETLQLLVAMLNRGVHPVVPCRGSVGASGDLAPLAHLALVLTGEGEAEVGGE 172 +G+SG+R TL+ L A+LN GV PVVP +GSVGASGDLAPL+HLA+VL G GEA GE Sbjct: 128 MRGHSGIRVATLRALAALLNSGVVPVVPEKGSVGASGDLAPLSHLAIVLLGGGEAFYQGE 187 Query: 173 VLPGAAALARAGLEPIRLGAKEGLALINGTQAMSALGALTVHRAQRLAKLADLACAMTLE 232 LPGA AL R GL PIRL KEGLAL NGT M A AL + + L ADLA AMTL+ Sbjct: 188 RLPGAEALERVGLAPIRLSFKEGLALNNGTAQMLATAALALDTLEYLLDTADLAAAMTLD 247 Query: 233 ATLGSRSAFLPHFHRLRPHPGQQSSARNLLVLTEDSALI--------------------- 271 A G A P H LRPHPGQ +A ++ L +S L+ Sbjct: 248 AFAGRSGALRPEVHALRPHPGQVETAGHVRDLLTESTLVDIPYHLVPRFKQWAADAWTAP 307 Query: 272 -----ASHAGCDRV-------QDAYSLRCAP-------------------QVHGASLDAI 300 + G D V ++A+ R P QVHGA DA Sbjct: 308 EDQALSFDIGWDWVPANQRHGREAFYSRFLPFKGGKKHQPQDAYCLRCMPQVHGAVRDAW 367 Query: 301 SYAAGVIAIEINSVTDNPLIFADT-------GQVVTGGHFHGQPVAMASDVLAIALAELA 353 + A VI IE+N+VTDNPLIF D QV++ GHFHG P+A+A + A+ LA Sbjct: 368 AQACRVIDIELNAVTDNPLIFPDAEGAQFIEEQVISAGHFHGMPLALAMSYVKAAIPVLA 427 Query: 354 DISERRTERLVNADYSNGLPMFLT-EAGGLHSGYMVAQYTAASLVSENKVLAHPACVDSI 412 ISERR +LV+ ++GLP FLT G SG+M+ QYTAA+LV++ AHPA V S+ Sbjct: 428 SISERRLNKLVDPATNDGLPAFLTGNEDGTDSGFMIVQYTAAALVNDLATRAHPASVYSV 487 Query: 413 PTSAGQEDHVSMGLTAARKAVTVCDNCERVIAIELMCAAQALDLR 457 PTSA EDHVSMG AR + + D+ VIA+EL AAQALD R Sbjct: 488 PTSANAEDHVSMGANEARHVLEMLDDLSHVIALELYTAAQALDFR 532 Lambda K H 0.320 0.135 0.384 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: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 514 Length of database: 629 Length adjustment: 36 Effective length of query: 478 Effective length of database: 593 Effective search space: 283454 Effective search space used: 283454 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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