Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate HSERO_RS18505 HSERO_RS18505 histidine ammonia-lyase
Query= curated2:Q7NCB3 (514 letters) >FitnessBrowser__HerbieS:HSERO_RS18505 Length = 526 Score = 277 bits (709), Expect = 6e-79 Identities = 176/451 (39%), Positives = 245/451 (54%), Gaps = 9/451 (1%) Query: 15 LAVDDLVAVARGGVPVRL--SPASLELVRRSRAFVEALLEGDEIVYGITTGFGYFKNRRI 72 LA++D+VA+AR +L +P + R F++ LL D +YG+TTG+G + Sbjct: 22 LAIEDVVALARRERSAQLHDAPDFRARIARGADFLDRLLREDGTIYGVTTGYGDSCTVTV 81 Query: 73 PRSAVEQLQQNLLMSSAAGLGEPFGREVVRAMLLLRANTLAQGYSGVRPETLQLLVAMLN 132 P V +L +L GLG F E RA+L R N+L QG+SGV L+ + +L Sbjct: 82 PPELVPELPHHLYTYHGCGLGALFTPEQARAILAARLNSLCQGFSGVSVALLEQITGLLQ 141 Query: 133 RGVHPVVPCRGSVGASGDLAPLAHLALVLTGEGEAEVGGEVLPGAAALARAGLEPIRLGA 192 + P +PC GSVGASGDL PL++LA VL GE + G +P A ALA AG+ P+RL Sbjct: 142 HDLLPQIPCEGSVGASGDLTPLSYLAAVLCGERDVWREGATVPAAQALAAAGMTPLRLRP 201 Query: 193 KEGLALINGTQAMSALGALTVHRAQRLAKLADLACAMTLEATLGSRSAFLPHFHRLRPHP 252 KEGLA++NGT M+AL L RA+ L +LA AM+ G+ F +PHP Sbjct: 202 KEGLAIMNGTAVMTALACLAFDRARYLCQLATRITAMSSFTLDGNAHHFDATLFSAKPHP 261 Query: 253 GQQSSARNLLVLTEDSALIASHAGCDRVQDAYSLRCAPQVHGASLDAISYAAGVIAIEIN 312 GQQ A L D +H R+QD YS+RCAP V G DA+ I E+N Sbjct: 262 GQQQVA---AWLQRDLPCGQAHRNEKRLQDRYSVRCAPHVIGVLNDALPSLRQFIENELN 318 Query: 313 SVTDNPLIFADTGQVVTGGHFHGQPVAMASDVLAIALAELADISERRTERLVNADYSNGL 372 S DNPLI D +V+ GGHF+G +A A D + A+A +AD+ +R+ +V+ Y+NGL Sbjct: 319 SANDNPLIDPDGERVLHGGHFYGGHIAFAMDSMKTAVANVADLLDRQMALMVDQRYNNGL 378 Query: 373 PMFLTEAGG----LHSGYMVAQYTAASLVSENKVLAHPACVDSIPTSAGQEDHVSMGLTA 428 P L+ A G ++ G Q +A++ +E L PA V S T +D VSMG A Sbjct: 379 PANLSGAQGARAPINHGLKALQISASAWTAEALKLTMPASVFSRSTECHNQDKVSMGTIA 438 Query: 429 ARKAVTVCDNCERVIAIELMCAAQALDLRGK 459 AR + V + E+V A L+ Q + LR + Sbjct: 439 ARDCLRVLELTEQVAAALLITVRQGVWLRSQ 469 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: 540 Number of extensions: 26 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: 526 Length adjustment: 35 Effective length of query: 479 Effective length of database: 491 Effective search space: 235189 Effective search space used: 235189 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