Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate Synpcc7942_0612 Synpcc7942_0612 methylcitrate synthase
Query= BRENDA::P45858 (372 letters) >FitnessBrowser__SynE:Synpcc7942_0612 Length = 386 Score = 243 bits (619), Expect = 8e-69 Identities = 143/370 (38%), Positives = 207/370 (55%), Gaps = 8/370 (2%) Query: 1 MEEKQHYSPGLDGVIAAETHISYLDTQSSQILIRGYDLIELSETKSYLELVHLLLEGRLP 60 M + PGL+GV A + IS++D Q + RG + +L++ S+LE +LL+ G LP Sbjct: 1 MTAVSEFRPGLEGVPATLSSISFVDGQRGVLEYRGISIEQLAQQSSFLETAYLLIWGHLP 60 Query: 61 EESEMETLERKINSASSLPADHLRLLELLPEDTHPMDGLRTGLSALAGY--DRQIDDRSP 118 + E+ E +I + +++ P+ HPMD L+ +AL + R +DD P Sbjct: 61 TQQELTEFEHEIRYHRRIKFRIRDMMKCFPDSGHPMDALQASAAALGLFYSRRALDD--P 118 Query: 119 SANKERAYQLLGKMPALTAASYRIINKKEPILPLQTLSYSANFLYMMTGKLPSSLEEQIF 178 + +LL K+P + AA I +PI P L Y+ANFLYM+T + P + +IF Sbjct: 119 EYIRAAVVRLLAKIPTMVAAFQLIRKGNDPIQPRDELDYAANFLYMLTEREPDPVAARIF 178 Query: 179 DRSLVLYSEHEMPNSTFAARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAK 238 D L L++EH + STF+A V AST +D Y + AV +L G LHGGANE V+ +L Sbjct: 179 DICLTLHAEHTINASTFSAMVTASTLTDPYAVVASAVGTLAGPLHGGANEEVLDMLEAIG 238 Query: 239 TTSDFEQLLQTKLKRKEKIMGFGHRVYMKKMDPRALMMKEALQQLCDKAGDHRLYEMCEA 298 + + E L + K +IMGFGHRVY K DPRA++++ +QL D G YE+ A Sbjct: 239 SVENVEPYLDHCIATKTRIMGFGHRVY-KVKDPRAVILQNLAEQLFDIFGHDPYYEIAVA 297 Query: 299 GERLMEK---EKGLYPNLDYYAAPVYWMLGIPIPLYTPIFFSARTSGLCAHVIEQHANNR 355 E+ + KG+YPN+D+Y+ VY LGIP L+TP+F AR +G AH EQ NR Sbjct: 298 VEKAAAERLSHKGIYPNVDFYSGLVYRKLGIPSDLFTPVFAIARVAGWLAHWKEQLNENR 357 Query: 356 LFRPRVSYMG 365 +FRP Y G Sbjct: 358 IFRPTQIYTG 367 Lambda K H 0.317 0.134 0.381 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: 341 Number of extensions: 13 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: 372 Length of database: 386 Length adjustment: 30 Effective length of query: 342 Effective length of database: 356 Effective search space: 121752 Effective search space used: 121752 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 (21.7 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