Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_012170314.1 AZC_RS09265 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000010525.1:WP_012170314.1 Length = 537 Score = 215 bits (548), Expect = 3e-60 Identities = 167/517 (32%), Positives = 254/517 (49%), Gaps = 29/517 (5%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62 +R+ +FDTTLRDG QT GV T+ +K+ + L+ GVD +EAG+P A+ + + Sbjct: 10 ERLYLFDTTLRDGAQTNGVDFTLADKLNVIGLLNRLGVDYVEAGYPGANPTDTQLFAQKR 69 Query: 63 GEELDAEICGLA----RCVKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116 G+ R V D + A + A+ D + S +R LE + EE L Sbjct: 70 PSAARVTAFGMTKRAGRSVSNDPGVAALLAAEADAICFVAKASAFQVRVALETTEEENLA 129 Query: 117 RAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTP 173 E V A G E D + + D+ L +A +AGA V + DT G P Sbjct: 130 SIRESVAAAVAAGREALVDCEHFFDGFKENPDFALACAEAAYQAGARWVVLCDTNGGTLP 189 Query: 174 PEMYRLTAEVVDAVDVP-VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNAS 232 E+ + A V V V +H HND AVANSLAAV AGA Q+ T+NG+GER GNA+ Sbjct: 190 HEVEAIVARVTARVPGSHVGIHAHNDTEQAVANSLAAVRAGARQIQGTLNGLGERCGNAN 249 Query: 233 LEQVVMALKALYD----IELDVRTEMLVEL---SRLVERLTGVVVPPNTPIVGENAFAHE 285 L ++ L D E V E L E+ SR ++ + + P VGE+AFA + Sbjct: 250 LCSLIPTLLLKGDYAERFETGVSREALAEIGVVSRTLDEMLNRSPDRHAPYVGESAFATK 309 Query: 286 SGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--TEEQLDE 343 +GIH+ ++K TYE + PE VG++RR+++ AGR + +LE +G+ V + +L Sbjct: 310 AGIHASAILKDPATYEHVPPEAVGNQRRVLVSDQAGRSNVLAELERLGVPVDRADPRLAR 369 Query: 344 IVRRVKELGDKG--KRVTEDDLEAIARDVVGEVPE----SEAAVKLEEIAVMTGNKFT-P 396 ++ VKE G + +AR ++ VP+ +VK+E G T Sbjct: 370 LLDEVKEREALGYAYEAADASFALLARRMLHSVPDFFTVERFSVKVERRYNAKGEMTTVA 429 Query: 397 TASVRVYLDGEEHEAASTGVGSVDAAIRALREAI---EELGMDVELKEYRLEAITGGTDA 453 A V+V + E +A+ G G V+A ALR+ + + + L +YR+ + GGT+A Sbjct: 430 EAIVKVRVGDEVFISAAEGNGPVNALDVALRKDLGKYQPYIAGLRLTDYRVRILNGGTEA 489 Query: 454 LAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 + V V DE G T G + +I+ AS +A + + Sbjct: 490 VTRVLVESTDESGARWTTVGVSPNIIDASFEALLDSI 526 Lambda K H 0.315 0.133 0.364 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: 553 Number of extensions: 26 Number of successful extensions: 4 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: 499 Length of database: 537 Length adjustment: 35 Effective length of query: 464 Effective length of database: 502 Effective search space: 232928 Effective search space used: 232928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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