Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Echvi_2056 Echvi_2056 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Cola:Echvi_2056 Length = 564 Score = 180 bits (456), Expect = 2e-49 Identities = 159/531 (29%), Positives = 241/531 (45%), Gaps = 28/531 (5%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLP--GSGIRHVLTRHEQGAGFMADGYA 87 + + +++ L + D +FG PG + +Y L I+HVLTRHEQGA A GYA Sbjct: 6 IRGAEIVIKSLVSENCDYIFGYPGGAIMPVYDALYDYADQIKHVLTRHEQGAIHAAQGYA 65 Query: 88 RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 RVSGK GVC +GPG TN+ T I A DS PL+ I+ SA LG ET D Sbjct: 66 RVSGKVGVCMATSGPGATNLITGIADALIDSTPLVCITGQVASALLGT--DAFQET-DVV 122 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 + P T ++ E + IA+ + + S RP PV I I D ++ + Sbjct: 123 GFSMPGTKWNIQVRKAEDIAPAIAKGFHIARSGRPGPVLIDITKDAQNELADFNYVPCLG 182 Query: 208 RRPGRGVP--CSEALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSERLAAPLFTSV 263 R R P + AAAE + AA+RP L+ G G + A E L A ++ P ++ Sbjct: 183 IRSYRPYPKVKDSEIAAAAEVINAAKRPYLLFGQGVVIGKAEEELKAFLDKTGIPAACTL 242 Query: 264 AGKGLLPPDAPL---NAGASLCVAPGWEMIAEADLVLAVGTEMAD-TDFWRERLPLSGEL 319 G G L + P G AP + + D+++AVG D +R ++ Sbjct: 243 LGSGALSEEHPQFVGKLGMHGNYAPN-ILTNKCDVLIAVGMRFDDRVTGDLKRYAKQAKV 301 Query: 320 IRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAH 379 + +++D + N V++ G+ +++L L ++ + + D A R L + ++A Sbjct: 302 VHLELDNAEINKNVKCEVSVLGNCKESLPMLTEKVNKASHDEWLAEFRT--LEEKEKSAV 359 Query: 380 APLQALHQ-------AILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGY 432 L L ++ I DA + TD+ Q F + R+ + G Sbjct: 360 VSLDLLPTKTGLTMGEVIRYINDYKKDDAVLVTDVGQHQMIAWRYFKFKTTRTQVTSGGL 419 Query: 433 GTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALG 492 GT+G+ LPA +GA+L R + +VGDGG T QEL T + SP+ V+L NN+ LG Sbjct: 420 GTMGFSLPAALGAQLADLNRQVVCVVGDGGIQMTVQELGTIM-QTRSPVKVVLLNNNFLG 478 Query: 493 QIRD-DMLGLDIEPVGVLPRNPDFALLGRAY---GCAVRQPQDLDELERDL 539 +R L D NPDF + AY V + DL + D+ Sbjct: 479 MVRQWQQLFFDKRYSFTELDNPDFIKIAEAYNMKATKVTERGDLSDAVADM 529 Lambda K H 0.321 0.136 0.412 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: 654 Number of extensions: 33 Number of successful extensions: 4 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: 559 Length of database: 564 Length adjustment: 36 Effective length of query: 523 Effective length of database: 528 Effective search space: 276144 Effective search space used: 276144 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: 53 (25.0 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