Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate PP_3723 PP_3723 putative 2-ketoarginine decarboxylase AruI
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__Putida:PP_3723 Length = 535 Score = 216 bits (550), Expect = 2e-60 Identities = 163/548 (29%), Positives = 266/548 (48%), Gaps = 30/548 (5%) Query: 4 LSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLAR 63 L+ + +VR L + GV+ VFG PG L++Y L GI HVL RHEQ A MADG AR Sbjct: 6 LTAGQALVRLLANYGVETVFGIPGVHTLELYRGLPG-SGIRHVLTRHEQGAGFMADGYAR 64 Query: 64 ATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLI--GYDAFQEC-DMVG 120 +G+ GV V +GPG TN T I AY DS+P++V+S T+ + G+ E D Sbjct: 65 VSGKPGVCFVITGPGVTNVATPIGQAYADSVPMLVISSVNHTASLGKGWGCLHETQDQRA 124 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 ++ P+ S + Q +D+P+++ +A+ + S RP PV + +P D+L A + W V Sbjct: 125 MTAPITAFSAVALQGDDLPELIARAWAVFDSERPRPVHISVPLDVL--AASVSRDWSGEV 182 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 R + +++A L AA++P++ GGGA+ A +QL++ L P+ S Sbjct: 183 VRRPGRGQPC--RETLEQAALKLAAAQRPMIIAGGGALHAA--EQLQQLSTRLAAPLFTS 238 Query: 241 LMGLGAFPA-THRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCP-NA 298 + G G P A L + ++ + ADV+ AVG D T+ + P Sbjct: 239 VAGKGLLPPDAPLNAGASLCVEPGWQ---LISQADVVLAVGTEMAD--TDFWRERLPIRG 293 Query: 299 TVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWR 358 +L +DIDP + I + GDARQ L+ +LE H P + Sbjct: 294 ELLRVDIDPRKFNDFYPCAIALQGDARQTLDGLLE-------HLPALQRDPAQASAAVAT 346 Query: 359 ARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418 RQ ++ + QA+++ + + DA+++SD+ Q + PR W++ Sbjct: 347 LRQAIRNGHAPLQATHQAILDRIAAVLPDDAFISSDMTQLAYTGNYAFASRAPRSWLHPT 406 Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTAL-QYELPVLVVNLNNRY 477 G GT+G+GLPA +G A + + GDG QEL+TA+ + P++V+ NN Sbjct: 407 GYGTLGYGLPAGIGGMFASDHRPGLVLVGDGGFLYTAQELATAVEELHRPLVVLLWNNDA 466 Query: 478 LGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRN 537 LG ++ DM+ + PDF+ LA A+ G + P +L++ ++ Sbjct: 467 LGQIR--DDMLGLDIEPVGVLPRNPDFIGLARAF---GCTVHQPRDLDALQADLASGFAT 521 Query: 538 NRLVFVDV 545 + F+++ Sbjct: 522 PGVTFIEL 529 Lambda K H 0.319 0.135 0.403 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: 764 Number of extensions: 55 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: 574 Length of database: 535 Length adjustment: 36 Effective length of query: 538 Effective length of database: 499 Effective search space: 268462 Effective search space used: 268462 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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