Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate N515DRAFT_0378 N515DRAFT_0378 acetolactate synthase, large subunit (EC 2.2.1.6)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Dyella79:N515DRAFT_0378 Length = 547 Score = 206 bits (525), Expect = 1e-57 Identities = 165/537 (30%), Positives = 252/537 (46%), Gaps = 25/537 (4%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARV 89 + A V+ L GV +FG+PG L+L L S I ++TRHEQ AGFMA + R+ Sbjct: 1 MNAAALFVKALEAEGVRRIFGVPGEENLDLVEALRDSKIELIVTRHEQAAGFMAATWGRL 60 Query: 90 SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149 +G+ GV GPG TN+ TA A ++P+L+I+ + +G L + D M Sbjct: 61 TGEAGVALSTLGPGATNLVTAAAYAQLGAMPMLMITGQKPIRTHKQG---LFQLVDVVDM 117 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPV--AHDWSAAVA 207 P+T ++ +S +P + A+ + ERP VH+ +P D+ V A A Sbjct: 118 MQPLTKYTRQIVSAPTIPARVREAFRRAEEERPGAVHLELPEDIARDSVDEAILLPTEYA 177 Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGA--LAAGEALAALSERLAAPLFTSVAG 265 RRP P AL A E + AA+ P+L+ G A AL ++L P FT+ G Sbjct: 178 RRPS---PDDAALVQAGEAITAAKHPILMIGAAANRQRTAVALRTFIDKLGIPFFTTQMG 234 Query: 266 KGLLPPDAPLNAGASLCVAPG---WEMIAEADLVLAVGTEMAD-TDFWRERLPLSGELIR 321 KG++ D PL G + ++ G I AD+++ VG ++ + F+ + + +I Sbjct: 235 KGVVDEDHPLWLG-NAALSDGDFVHRAIDAADVIVNVGHDVVEKPPFFMHKGRRT--VIH 291 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHA- 380 ++ + + Y + + GD T+E L L +A + +V A HA Sbjct: 292 INFSSAEVDTVYFPQIEVVGDIAHTVERLTDALTPQAHWNFKYFDQVREAFHRQLAEHAD 351 Query: 381 -PLQALHQA-ILDRIAAALPADAFVSTD--MTQLAYTGNYAFASRAPRSWLHPTGYGTLG 436 P +H ++ +P D + D M ++ Y Y +R P + L T+G Sbjct: 352 DPRFPIHPVRLVADTRRYMPDDGVLCLDNGMYKIWYARYY--RARQPNTVLLDNALATMG 409 Query: 437 YGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRD 496 GLP+ + AKL P+R L + GDGGF+ AQEL TA L LV+LL +DA G IR Sbjct: 410 AGLPSAMAAKLVYPERKVLAICGDGGFMMNAQELETA-VRLKMDLVILLLRDDAYGMIRW 468 Query: 497 DMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 + G+ NPDF A+G +P+ D L+ F Q GV LI+L Sbjct: 469 KQAEMGYADFGMQFSNPDFVKFAEAHGAHGHRPESADAFLPTLKRAFEQGGVHLIDL 525 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: 641 Number of extensions: 35 Number of successful extensions: 5 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: 547 Length adjustment: 36 Effective length of query: 523 Effective length of database: 511 Effective search space: 267253 Effective search space used: 267253 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