Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 7026738 Shewana3_3871 ornithine decarboxylase (RefSeq)
Query= BRENDA::P28629 (755 letters) >FitnessBrowser__ANA3:7026738 Length = 720 Score = 320 bits (819), Expect = 2e-91 Identities = 206/633 (32%), Positives = 317/633 (50%), Gaps = 35/633 (5%) Query: 121 DFIAGRAVAAMTRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDY 180 DF + A+ +Y Q LLPP F L KY ++ ++A PGHQGG F K P GR + D+ Sbjct: 90 DFYGKQVETAVQKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDF 149 Query: 181 YGENLFRTDMGIERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQA 240 +GE +FR+DM LG LL H GA +++KYAA+VF AD+++ V+ GTS SN+ A Sbjct: 150 FGETIFRSDMCNADVKLGDLLIHEGAPLDAQKYAAKVFNADKTYFVLNGTSSSNKVATNA 209 Query: 241 CMTDNDVVVVDRNCHKSIEQG-LMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKI 299 + D+V+ DRN HKS G L+ GA P+Y+ +RN +G IG I Q L+++I Sbjct: 210 LLAKGDLVLFDRNNHKSNHHGALIQAGATPIYLETARNPFGFIGGIDAHCFQESYLREQI 269 Query: 300 -SESPLTKDKAGQKP-SYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFN 357 + +P D+ Q+P ++ TYDG YNA++ D + D + FD AW GY +F Sbjct: 270 RAVAPERADE--QRPFRLAIIQLGTYDGTIYNARQVVDRIGHLCDYILFDSAWVGYEQFI 327 Query: 358 PIYADHYAMRGE--PGDHNGPTVFATHSTHKLLNALSQASYIHVREGR-----GAINFSR 410 P+ D + E P D P + T S HK SQ S IH ++ N R Sbjct: 328 PMMNDCSPLLLELTPED---PGIIVTQSVHKQQAGFSQTSQIHKKDSHIKGQARYCNHKR 384 Query: 411 FNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTA 470 FN A+MMHA+TSP Y + A+ DV M +G SG L +E + ++ R+ + + K Sbjct: 385 FNNAFMMHASTSPFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCK---- 440 Query: 471 DGSWFFKPWNKEVVTDPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSM 530 + KP+ ++ G+ + D PT+ + + PG+ WH F Sbjct: 441 ----YIKPFIPSMI----EGRPWQ--DYPTEQMADDLRFFEFEPGQKWHSFDGYEKGQYF 490 Query: 531 LDPIKVSILAPGM-GEDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRG 589 +DP K + PG+ E G+ E G+PA ++ +L + I+P + I+FL + Sbjct: 491 VDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDMA 550 Query: 590 KWGTLVNTLCSFKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGA 649 K LV+ + F++ D + PL++V+P + Y + I L M ++ Sbjct: 551 KMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVKQ 610 Query: 650 RLNEAY--SGLPVAEVTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSG 707 E + + P + P+EA + VELV + + GRIAA +PYPPG+ ++ G Sbjct: 611 LQKEMFRQAHFPTKVMDPQEANLEFIRGKVELVPLSQIEGRIAAEGALPYPPGVLCVVPG 670 Query: 708 ENFGDKNSPQVSYLRSLQSWDHHFPGFEHETEG 740 E +G Y +L+ + PGF E +G Sbjct: 671 EIWG---GAVQRYFLALEEGINLLPGFSPELQG 700 Lambda K H 0.319 0.135 0.414 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: 1257 Number of extensions: 60 Number of successful extensions: 8 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: 755 Length of database: 720 Length adjustment: 40 Effective length of query: 715 Effective length of database: 680 Effective search space: 486200 Effective search space used: 486200 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: 55 (25.8 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