Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 6939240 Sama_3334 ornithine decarboxylase (RefSeq)
Query= BRENDA::P28629 (755 letters) >FitnessBrowser__SB2B:6939240 Length = 720 Score = 324 bits (831), Expect = 9e-93 Identities = 208/675 (30%), Positives = 326/675 (48%), Gaps = 30/675 (4%) Query: 75 LIGKLHERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRY 134 ++ K+ N+P+F+ E+A D + + + DF + A+ RY Sbjct: 47 IVDKIKNTGLNLPIFVSVCCEEAFPD---DFCDTITGVFELCNAKTDFYGKQVETAVRRY 103 Query: 135 RQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIER 194 ++ LLPP F L KY ++ ++A PGHQGG F K P GR + D++GE +FR+DM Sbjct: 104 QESLLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETVFRSDMCNAD 163 Query: 195 TSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNC 254 LG LL H GA +++ YAA+V+ AD+++ V+ GTS SN+ + A + D+V+ DRN Sbjct: 164 VKLGDLLIHEGAPHDAQAYAAKVYNADKTYFVLNGTSASNKVVCNALLAPGDLVLFDRNN 223 Query: 255 HKSIEQG-LMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKP 313 HKS G L+ GA PVY+ +RN +G IG I L+ +I + + +A + Sbjct: 224 HKSNHHGALIQAGATPVYLETARNPFGFIGGIDSHCFDEAYLRDEIGKVAPERVQAARPF 283 Query: 314 SYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDH 373 ++ TYDG YNA++ D + D + FD AW GY +F P+ D + E G Sbjct: 284 RLAIIQLGTYDGTIYNARQVVDRIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELGAE 343 Query: 374 NGPTVFATHSTHKLLNALSQASYIHVREG-----RGAINFSRFNQAYMMHATTSPLYAIC 428 + P + T S HK SQ S IH ++ N RFN A+MMHA+TSP Y + Sbjct: 344 D-PGIIVTQSVHKQQAGFSQTSQIHKKDSHIKGQERYCNHKRFNNAFMMHASTSPFYPLF 402 Query: 429 ASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVTDPQ 488 A+ DV M +G SG L +E + ++ R+ + + K + KP+ P Sbjct: 403 AALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCK--------YIKPF------IPT 448 Query: 489 TGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGM-GEDG 547 T + + T+ + + PG WH F +DP K + PG+ E G Sbjct: 449 TVEGEPWQSFDTERMADDLRFFEFEPGLKWHAFDGYEKGQYFVDPCKFLLTTPGINAETG 508 Query: 548 ELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRHYDA 607 E E+ G+PA ++ +L + I+P + I+FL + K LV + F++ D Sbjct: 509 EYEDFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDMAKMQHLVTQIARFEKLIDE 568 Query: 608 NTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAY--SGLPVAEVTP 665 + PL++V+P + + Y I L M N E + + P A + P Sbjct: 569 DAPLSEVLPNVYRTNRERYEGYSIRRLCQEMHDLYVSRNVKQLQKEMFRAAHFPKAVMNP 628 Query: 666 REAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLRSLQ 725 ++A A V ELV + + G+IAA +PYPPG+ ++ GE +G Y +L+ Sbjct: 629 QDANIAFVRGKAELVPLSEIEGQIAAEGALPYPPGVLCMVPGEVWG---GAVQRYFLALE 685 Query: 726 SWDHHFPGFEHETEG 740 + PGF E +G Sbjct: 686 EGINLLPGFAPELQG 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: 1262 Number of extensions: 65 Number of successful extensions: 7 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