Align Arginine decarboxylase; EC 4.1.1.19 (uncharacterized)
to candidate Synpcc7942_0707 Synpcc7942_0707 arginine decarboxylase
Query= curated2:Q9K9K5 (491 letters) >FitnessBrowser__SynE:Synpcc7942_0707 Length = 489 Score = 310 bits (795), Expect = 6e-89 Identities = 165/484 (34%), Positives = 282/484 (58%), Gaps = 5/484 (1%) Query: 8 PLFSGVVAHAKHNPVQFHIPGHKKGAGMDPAFRSFIGDNALSIDLINIGPLDDLHHPHGI 67 PLF ++A A+ FH PGHK G + + G DL + LD+L+ G+ Sbjct: 4 PLFDQLLASAQQARAPFHTPGHKLGRAIATHLQQAWGSAIFQSDLPELPELDNLYAASGV 63 Query: 68 IKEAQELAAEAFGADHTFFSVQGTSGAIMTMIMSVVGPGEKIIVPRNVHKSIMSAIVFSG 127 + E+Q AAE FGAD ++F V G++G ++ I+++ PG+++++PRN H+S++S + SG Sbjct: 64 LAESQAQAAEVFGADRSWFLVNGSTGGLLAAILTICSPGDRLLLPRNAHRSLLSGCILSG 123 Query: 128 ATPVFIHPEIDPLLGISHGITIEAVEKALDAHPDAKGLLVINPTYFGIAANLKKIVELCH 187 A PV+I P + T E V AL P K +++++PTY G+ A++ I + H Sbjct: 124 AMPVWITPPEAADFDLVGVPTPEQVATALAQDPQIKAVVLVSPTYEGVCADVAAIAAIAH 183 Query: 188 SRDVPVLVDEAHGVHIHFHEALPLSAMQAGADMAATSVHKLGGSLTQSSILNVREGLVSA 247 + ++P+++D AHG H+ FH LP S + GAD+ S HKL G+LTQ+++L+ + + Sbjct: 184 NHNLPLIIDAAHGAHLGFHPDLPRSPLHEGADLVVQSTHKLLGALTQAAMLHCKGDRIDP 243 Query: 248 KRVQTIISMLTTTSTSYLLLASLDAARKHLATNGRDLIGYTIQLADQARDQINAIDGLYC 307 +R+ ++++ ++S SYLLLASL+AA + + T+ +DL+ TI LA QA ++ + GL Sbjct: 244 ERLSQSLALVQSSSPSYLLLASLEAATEQMRTSAQDLLQVTIDLARQAHQRLAELPGLQL 303 Query: 308 VGKEILGTIATYDYDPTKLIISVKNLGITGYDAEVWLREHYQIEVELSDLYNILCIVSFG 367 +I +D T+L+I+ ++ G +G+ A+ +L E +Q+ EL L N++ +S G Sbjct: 304 PALKIGNREGFPQWDRTRLVINFQSCGWSGFCADEYLHEQWQVTAELPSLSNLVFHLSLG 363 Query: 368 DTEREMDLLVKALSE-LADLHKHGICERSPVSVYVPNIPTLAMSPRDAFYAETEVVPFED 426 + ++D LV A L+ H+ + R PV + P +SPR A+++ + V E Sbjct: 364 NRIEDIDRLVTACDRLLSQEHQEELPPRLPVWLE----PETILSPRQAWFSRHQTVSAEQ 419 Query: 427 SVGRTIAEFIMVYPPGIPILIPGEIITESNLAYIRENNRAGLPVQGPEDDTFRTLRVIKE 486 ++G AE + YPPGIP+L+PGE I++S + Y+R+ G + G D TLR++++ Sbjct: 420 AIGAIAAECVCPYPPGIPVLLPGERISKSAVDYLRQVQTTGGILSGCADPELTTLRIVQD 479 Query: 487 HEAI 490 + I Sbjct: 480 SDTI 483 Lambda K H 0.320 0.137 0.398 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: 472 Number of extensions: 19 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: 491 Length of database: 489 Length adjustment: 34 Effective length of query: 457 Effective length of database: 455 Effective search space: 207935 Effective search space used: 207935 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