Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate 6939201 Sama_3295 methylcitrate synthase (RefSeq)
Query= SwissProt::Q8EJW2 (375 letters) >FitnessBrowser__SB2B:6939201 Length = 378 Score = 674 bits (1738), Expect = 0.0 Identities = 327/371 (88%), Positives = 348/371 (93%) Query: 5 KKLTGAGLRGQSAGETALSTVGVSGSGLTYRGYDVKDLAENATFEEVAYLILYGELPTTA 64 KKL+GAGLRGQSAGETALSTVG SGSGLTYRGYDVKDLAENA+FEEVA+LILYGELPT Sbjct: 7 KKLSGAGLRGQSAGETALSTVGKSGSGLTYRGYDVKDLAENASFEEVAFLILYGELPTQL 66 Query: 65 QLAAYKTKLKGMRGLPQALKEVLERIPADAHPMDVMRTGCSMLGNLEAEHSFSEQSQIAD 124 +L Y+ KLKG+RGLPQALKEVLERIPA+AHPMDV+RTGCSMLGNLE EHSF++Q + + Sbjct: 67 ELDNYRAKLKGLRGLPQALKEVLERIPANAHPMDVLRTGCSMLGNLETEHSFADQFDVTN 126 Query: 125 RLLAAFPSIICYWYRFSHDGVRIDTETDDDQIGAHFLHLLHGKAPSALHTKVMDVSLILY 184 R+LA FPSIICYWYRFSHDGVRI+TETDD+QIGAHFLHLLHGKAPSALH +VMDVSLILY Sbjct: 127 RMLAVFPSIICYWYRFSHDGVRIETETDDEQIGAHFLHLLHGKAPSALHARVMDVSLILY 186 Query: 185 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMKDEADARD 244 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDM+DE ARD Sbjct: 187 AEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMRDEQHARD 246 Query: 245 VLMGKLERKEKIMGFGHAIYRDSDPRNAIIKEWSEKLAADYGDDRLYRVSVACEALMWEQ 304 VL G LERKEKIMGFGHAIYR+SDPRNAIIKEWSEKLA +YGDDRLYRVSVACEA MWEQ Sbjct: 247 VLAGMLERKEKIMGFGHAIYRESDPRNAIIKEWSEKLAKEYGDDRLYRVSVACEAFMWEQ 306 Query: 305 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWTAHVMEQRSNNRIIRPSADYVGV 364 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRV+GWTAHVMEQRSNNRIIRPSADYVGV Sbjct: 307 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVSGWTAHVMEQRSNNRIIRPSADYVGV 366 Query: 365 SPRKVIPIANR 375 R V PI+ R Sbjct: 367 ELRSVTPISER 377 Lambda K H 0.320 0.134 0.401 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: 573 Number of extensions: 13 Number of successful extensions: 1 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: 378 Length adjustment: 30 Effective length of query: 345 Effective length of database: 348 Effective search space: 120060 Effective search space used: 120060 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: 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