Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate Echvi_3057 Echvi_3057 citrate synthase I (hexameric type)
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >FitnessBrowser__Cola:Echvi_3057 Length = 428 Score = 201 bits (510), Expect = 4e-56 Identities = 129/389 (33%), Positives = 204/389 (52%), Gaps = 29/389 (7%) Query: 11 GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70 G + + ++A++ + L YRGY++ DLA + F EV+YLL+YGELPTQ Q D + Sbjct: 45 GFKNTGSTKSAITFLDGEKGILRYRGYNIEDLAEKSNFLEVSYLLIYGELPTQEQYDQFA 104 Query: 71 GKLRQLRDLPQALKEVLERIPADAHPMDVMRT-GCSFLG----NLEPEQDFSQQHDKTDR 125 ++ + + +K++L+ P+ AHPM V+ + CS +L+P + + R Sbjct: 105 NEITYHTLVHEDIKKILDGFPSVAHPMGVLSSLICSLTAFYPTSLDPNRTDEEIKLSIVR 164 Query: 126 LLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVS 180 L+A P + Y+ + G + + +F+ ++ + V K ++ Sbjct: 165 LMAKLPTFAAWAYK-NKMGHPANYPDNSLDYCSNFMKMMFALPAEKYEVDPIIAKALDKL 223 Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240 LIL+A+HE N ST T R+ S+ + +++ I+A I +L GPLHGGAN++ +EM+E Sbjct: 224 LILHADHEQNCSTSTVRIVGSSQASIYASISAGINALWGPLHGGANQSVIEMLEAIKEDG 283 Query: 241 EAIEGTLGMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADE------VGDTVLF 291 + L K+ ++MGFGH +YK+ DPR ++I KK AD+ V D VL Sbjct: 284 GDTKKYLDKAKDKNDPFRLMGFGHRVYKNFDPRAKII----KKAADDVLGKLGVNDPVLE 339 Query: 292 PVSE----AIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE 347 E A++ + +KL+PN DFY Y +GIPT +FT +F RL GW A E Sbjct: 340 IAKELEEAALNDQYFVDRKLYPNVDFYSGIIYRALGIPTDMFTVMFALGRLPGWIAQWKE 399 Query: 348 QRANNRII-RPSAEYTGVEQRKFVPIEQR 375 R NN I RP YTG +R +V + R Sbjct: 400 MRENNEPIGRPRQVYTGPNERSYVSMGDR 428 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: 373 Number of extensions: 16 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: 375 Length of database: 428 Length adjustment: 31 Effective length of query: 344 Effective length of database: 397 Effective search space: 136568 Effective search space used: 136568 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 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