Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate PfGW456L13_242 Putative histidine ammonia-lyase protein
Query= curated2:Q7NCB3 (514 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_242 Length = 514 Score = 275 bits (703), Expect = 3e-78 Identities = 178/497 (35%), Positives = 263/497 (52%), Gaps = 13/497 (2%) Query: 15 LAVDDLVAVARGGVPVRLS--PASLELVRRSRAFVEALLEGDEIVYGITTGFGYFKNRRI 72 L ++D++A+A VP +L PA E + + F+++LL+ + ++YG+TTG+G + Sbjct: 16 LRIEDVLALANRKVPTQLQSDPAYRERIAKGARFLDSLLDKEGVIYGVTTGYGDSCVVAV 75 Query: 73 PRSAVEQLQQNLLMSSAAGLGEPFGREVVRAMLLLRANTLAQGYSGVRPETLQLLVAMLN 132 P VE L ++L GLG+ + RA+L R +L G SGVR E L+ L A L Sbjct: 76 PLHHVEALPRHLYTFHGCGLGKLLDAQATRAVLAARLQSLCHGVSGVRVELLERLQAFLE 135 Query: 133 RGVHPVVPCRGSVGASGDLAPLAHLALVLTGEGEAEVGGEVLPGAAALARAGLEPIRLGA 192 + P++P GSVGASGDL PL+++A L+GE E GE A G +P+ L Sbjct: 136 HDILPLIPEEGSVGASGDLTPLSYVAATLSGEREVMFRGERRQAADVHRELGWQPLVLRP 195 Query: 193 KEGLALINGTQAMSALGALTVHRAQRLAKLADLACAMTLEATLGSRSAFLPHFHRLRPHP 252 KE LAL+NGT M+ L L RA L LA A+ + A G+ F +PHP Sbjct: 196 KEALALMNGTAVMTGLACLAYARADYLLHLATRITALNVVALQGNPEHFDERLFATKPHP 255 Query: 253 GQQSSARNLLVLTEDSALIASHAGCDRVQDAYSLRCAPQVHGASLDAISYAAGVIAIEIN 312 GQ A L +D A+ A A R+QD YSLRCAP V G D++++ I IE+N Sbjct: 256 GQMQVA---AWLRKDLAIDAPTAPLHRLQDRYSLRCAPHVLGVLADSLNWLRSFIEIELN 312 Query: 313 SVTDNPLIFADTGQVVTGGHFHGQPVAMASDVLAIALAELADISERRTERLVNADYSNGL 372 S DNP+I A+ +V+ GGHF+G +A A D L +A +AD+ +R+ LV+ Y++GL Sbjct: 313 SANDNPIIDAEAERVLHGGHFYGGHIAFAMDSLKNLVANVADLLDRQLALLVDERYNHGL 372 Query: 373 PMFLTEAGG----LHSGYMVAQYTAASLVSENKVLAHPACVDSIPTSAGQEDHVSMGLTA 428 P L+ A L+ G+ Q ++ +E PA V S T +D VSMG A Sbjct: 373 PSNLSGATADRAMLNHGFKAVQIGTSAWTAEALKNTMPASVFSRSTECHNQDKVSMGTIA 432 Query: 429 ARKAVTVCDNCERVIAIELMCAAQALDLRGKLTPGRGSRVGLEVIRAAV----PHLESDR 484 AR A+ V + E+V A L+ A Q + LRG+ R L + A+ P + DR Sbjct: 433 ARDAIRVLELTEQVAAATLLAANQGVWLRGQAEDARPLPPALAAMHEALAKDFPPVIEDR 492 Query: 485 IVSRDIEKVVELMADGH 501 + ++ ++ +A+ H Sbjct: 493 ALEGELRLCLQRIAEQH 509 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: 553 Number of extensions: 27 Number of successful extensions: 3 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: 514 Length of database: 514 Length adjustment: 35 Effective length of query: 479 Effective length of database: 479 Effective search space: 229441 Effective search space used: 229441 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: 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