Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate AZOBR_RS04230 AZOBR_RS04230 indole-3-pyruvate decarboxylase
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__azobra:AZOBR_RS04230 Length = 545 Score = 124 bits (310), Expect = 1e-32 Identities = 137/486 (28%), Positives = 208/486 (42%), Gaps = 51/486 (10%) Query: 34 QALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLT-RHEQGAGFMADGYARVSGK 92 +AL+R L + G +FGIPG L ++ + I + T HE GF AD AR S Sbjct: 5 EALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSST 64 Query: 93 PGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHE---TQDQRAM 149 GV V G G N+ A+ AYA+ P++VIS + G H+ Q + Sbjct: 65 LGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDTQFQV 124 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAA---PVAHDWSAAV 206 IT A P + P IAR + RPV++ IP +++ A PV D + V Sbjct: 125 FKEITVAQARLDDPAKAPAEIARVLGAARA-LSRPVYLEIPRNMVNAEVEPVGDDPAWPV 183 Query: 207 ARRPGRGVPCSEALRAAAERLAAARR----PMLIAGGGALAAG--EALAALSERLAAPLF 260 R +AL A A+ + AA R P+L+ G +A L++RL P+ Sbjct: 184 DR---------DALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVV 234 Query: 261 TSVAGKGLL--PPDAPLNAGASLCVAPGWE---MIAEADLVLAVGTEMADTDFWRERLPL 315 T+ G+GLL P PL G + VA E ++ E+D + +G ++DT+F Sbjct: 235 TTFMGRGLLADAPTPPL--GTYIGVAGDAEITRLVEESDGLFLLGAILSDTNF------- 285 Query: 316 SGELIRVDIDPRKFNDFYPSAVALRGDARQTL------EALLVRLPQEARDSAPAAARVA 369 + + ID RK + AV L + +ALL RLP R + Sbjct: 286 --AVSQRKIDLRKTIHAFDRAVTLGYHTYADIPLAGLVDALLERLPPSDRTTRGKEPHAY 343 Query: 370 RLRAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHP 429 + + +A+ DR+ A ++ DM +T + P Sbjct: 344 PTGLQADGEPIAPMDIARAVNDRVRAG-QEPLLIAADMGDCLFTA----MDMIDAGLMAP 398 Query: 430 TGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNND 489 Y +G+G+PAGIGA+ + + L +VGDG F T EL L +V+L+NN Sbjct: 399 GYYAGMGFGVPAGIGAQCVSGGKRILTVVGDGAFQMTGWELGNC-RRLGIDPIVILFNNA 457 Query: 490 ALGQIR 495 + +R Sbjct: 458 SWEMLR 463 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: 733 Number of extensions: 34 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: 559 Length of database: 545 Length adjustment: 36 Effective length of query: 523 Effective length of database: 509 Effective search space: 266207 Effective search space used: 266207 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