Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate CCNA_02185 CCNA_02185 acetolactate synthase large subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Caulo:CCNA_02185 Length = 601 Score = 193 bits (490), Expect = 2e-53 Identities = 161/531 (30%), Positives = 244/531 (45%), Gaps = 30/531 (5%) Query: 28 KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGL-PGSGIRHVLTRHEQGAGFMADGY 86 + +T + +VR L + GV+ +FG PG L +Y L ++H+L RHEQGA A+GY Sbjct: 18 RAMTGAEIVVRGLVDQGVEVLFGYPGGAVLPIYDALFHEPRLQHILVRHEQGAAHAAEGY 77 Query: 87 ARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQ 146 AR SGKPGV V +GPG TN T I A DS+P++VI+ + +G + D Sbjct: 78 ARSSGKPGVVLVTSGPGATNAITGIMDALMDSIPMVVITGQVPTHLIGTD---AFQEADT 134 Query: 147 RAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAV 206 MT T + L LP++I A+ + + RP PV I IP DV A + V Sbjct: 135 VGMTRSCTKHNYLVKDVRDLPQIIHEAFKIATTGRPGPVLIDIPKDVQFAKGEYFGPGEV 194 Query: 207 ARRPG---RGVPCSEALRAAAERLAAARRPMLIAGGGALAAG-EALAALSERLA---APL 259 A R + + AA +A ARRP+ GGG + AG +A AAL E A AP+ Sbjct: 195 ASTHAYAPRTKGDAGRIAEAARMIAQARRPIFYTGGGVINAGPKASAALREFAALTGAPV 254 Query: 260 FTSVAGKGLLPPDAPLNAGASLCVAPGWE---MIAEADLVLAVGTEMADTDFWR-ERLPL 315 +++ G G P P G L + +E + + D+++ VG D R + Sbjct: 255 TSTLMGLGAFPAADPAWLG-MLGMHGTFEANNAMHDCDVMICVGARFDDRVTGRLDAFSP 313 Query: 316 SGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAA-----ARVAR 370 + I +DIDP N + + GDA LE L+ AA A++ + Sbjct: 314 GSKKIHIDIDPSSINKNVRVDLPIVGDAGSVLEDLIAAWKAANLQPNKAALTDWWAQIDQ 373 Query: 371 LRAEIRAAHAPLQAL--HQAILDRI-AAALPADAFVSTDMTQLAYTGNYAFASRAPRSWL 427 RA ++ ++ Q ++R+ D +++T++ Q F P W+ Sbjct: 374 WRARQCLSYRRSDSVIKPQYAIERLYELTKDKDVYITTEVGQHQMWAAQFFRFEEPNRWM 433 Query: 428 HPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWN 487 G GT+GYGLPA +G +L P + + G+ QEL+TA + D P+ + + N Sbjct: 434 TSGGLGTMGYGLPAALGVQLAHPNSLVVDIAGEASIQMCIQELSTAI-QFDLPVKIFILN 492 Query: 488 NDALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCA---VRQPQDLD 533 N+ +G +R +L + PDF L AYG P +LD Sbjct: 493 NEWMGMVRQWQQLLHGERYSHSYSDSLPDFVKLAEAYGAVGIRCDNPAELD 543 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: 822 Number of extensions: 42 Number of successful extensions: 6 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: 601 Length adjustment: 36 Effective length of query: 523 Effective length of database: 565 Effective search space: 295495 Effective search space used: 295495 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