Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate CA265_RS15805 CA265_RS15805 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Pedo557:CA265_RS15805 Length = 583 Score = 196 bits (497), Expect = 3e-54 Identities = 164/550 (29%), Positives = 253/550 (46%), Gaps = 27/550 (4%) Query: 25 QPQKTL---TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLP--GSGIRHVLTRHEQGA 79 + KTL T Q L+ L GV T+FG PG + +Y L + H+L RHEQG Sbjct: 16 ETSKTLFKGTGSQVLLNGLIEEGVTTIFGYPGGAIMPIYDALYDYADKLEHILVRHEQGG 75 Query: 80 GFMADGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGC 139 A G+AR SG+ GV F +GPG TN+ T + A DS PL+ I+ + LG Sbjct: 76 IHAAQGFARASGEVGVVFATSGPGATNLVTGLADAQIDSTPLVCITGQVFAHLLGT--DA 133 Query: 140 LHETQDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISI----PLDVLA 195 ET D +T P+T ++ +++ E++A+A+ + S RP PV I I L + Sbjct: 134 FQET-DVINITTPVTKWNYQVTDAKEIQEVLAKAFYIAKSGRPGPVLIDITKNAQLQLEE 192 Query: 196 APVAHDWSAAVARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSE 253 P + + RP V E + AAE + +A++P ++ G G + +A E A Sbjct: 193 FPEYVKCNHIRSYRPKPKVRI-EYIEQAAELINSAKKPFVLFGQGVILGSAEEEFKAFIN 251 Query: 254 RLAAPLFTSVAGKGLLPPDAPLNAG-ASLCVAPGWEMIA-EADLVLAVGTEMADTDFWR- 310 + P ++ G+G +P PLN G + G ++ EAD+++A+G D R Sbjct: 252 KTGIPAAWTIMGEGAIPTSHPLNVGMLGMHGNYGPNVLTNEADVIIAIGMRFDDRVTGRL 311 Query: 311 ERLPLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVAR 370 ++ ++ +DIDP + + + V + GD ++TL LL L E + A Sbjct: 312 DKYAKQARVVHLDIDPAEIDKNVKAEVGVWGDCKETL-PLLTNLVNENKHEDWLAKFRQY 370 Query: 371 LRAEIRAAHAPL------QALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPR 424 + EI P + +L I DA + TD+ Q R Sbjct: 371 NQEEIDQVITPELYPTGDEMTMGEVLRNINEICGGDAVIVTDVGQHQMVACRYAKFNNTR 430 Query: 425 SWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVL 484 S + G GT+G+GLPA IGAK GAP + + ++GDGGF T QEL T + + + +L Sbjct: 431 SNITSGGLGTMGFGLPAAIGAKYGAPDKTVIAIIGDGGFQMTPQELGTIM-QFGAAVKIL 489 Query: 485 LWNNDALGQIRD-DMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGF 543 + NN LG +R L D V +PDF L ++Y + + L + L Sbjct: 490 ILNNRFLGMVRQWQQLFHDKRYSFVNITSPDFVALAKSYYIEASKVDERANLRQALETMI 549 Query: 544 GQSGVTLIEL 553 G L+E+ Sbjct: 550 NHEGSYLLEV 559 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: 643 Number of extensions: 41 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: 559 Length of database: 583 Length adjustment: 36 Effective length of query: 523 Effective length of database: 547 Effective search space: 286081 Effective search space used: 286081 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