Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_028313015.1 H566_RS0121225 citrate synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_000482785.1:WP_028313015.1 Length = 436 Score = 179 bits (455), Expect = 1e-49 Identities = 124/389 (31%), Positives = 195/389 (50%), Gaps = 26/389 (6%) Query: 11 GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70 G + Q+A++ + L YRGY + LA F E YLLL GELP Q D + Sbjct: 50 GFLSTASCQSAITYIDGDKGELLYRGYPIEQLATKCDFLETCYLLLNGELPNATQKDDFV 109 Query: 71 GKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQ----DFSQQHDKTDRL 126 ++ Q + + + L DAHPM V+ + P+ D Q+ RL Sbjct: 110 ARVTQHTMVNEQMHFFLRGFRRDAHPMAVLTGLVGAMSAFYPDSMNLNDAHQREISAIRL 169 Query: 127 LAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGK-----KPSELHVKVMNVSL 181 +A P ++ Y++S GQ +++S +F ++ K +++ V+ ++ Sbjct: 170 IAKLPTLVAMAYKYSI-GQPFIYPHNDLSYTANFTRMMFATPCEEYKVNDVLVRALDRIF 228 Query: 182 ILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQE 241 IL+A+HE NAST T R+CAS+ ++ F+ I A + L GP HGGANEAA+ M+ + Q Sbjct: 229 ILHADHEQNASTSTVRLCASSGTNPFAAIAAGVACLWGPAHGGANEAALNMLYDIQA-QG 287 Query: 242 AIEGTLGMLAR-KDK-----IMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPV 293 +E +A+ KDK +MGFGH +YK+ DPR ++++ ++ +G + LF + Sbjct: 288 GVEKIGEFVAKVKDKNSGVRLMGFGHRVYKNYDPRAKLMRETCHEVLGALGLENDPLFKL 347 Query: 294 SEAIDKTMWE-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQ 348 + A++K E Q+KL+PN DFY +GIP LFT IF +R GW A + E Sbjct: 348 AMALEKIALEDDYFVQRKLYPNVDFYSGIVQKAIGIPVSLFTAIFALARTVGWIAQLNEM 407 Query: 349 RAN--NRIIRPSAEYTGVEQRKFVPIEQR 375 + +I RP +TG R + R Sbjct: 408 ITDPEYKIGRPRQLFTGAVTRNVPDLSAR 436 Lambda K H 0.321 0.135 0.406 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: 379 Number of extensions: 17 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: 375 Length of database: 436 Length adjustment: 31 Effective length of query: 344 Effective length of database: 405 Effective search space: 139320 Effective search space used: 139320 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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