Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate SMa2135 SMa2135 GlyA2 serine hydroxymethyltransferase, SHMT
Query= SwissProt::Q3JGP5 (424 letters) >FitnessBrowser__Smeli:SMa2135 Length = 422 Score = 548 bits (1412), Expect = e-160 Identities = 271/411 (65%), Positives = 321/411 (78%), Gaps = 2/411 (0%) Query: 14 ERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCE 73 + D+ + GAI +E+ RQ+S++ELIASENIVS AVL AQGSV+TNKYAEGYPG RYYGGC+ Sbjct: 10 KHDSVIAGAIAREMGRQRSEIELIASENIVSPAVLAAQGSVMTNKYAEGYPGHRYYGGCQ 69 Query: 74 FADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTH 133 + D VEA AIER LF+A NVQPHSGAQANGAVMLAL KPGDT +G+SL AGGHLTH Sbjct: 70 YVDLVEAAAIERAGMLFDASFVNVQPHSGAQANGAVMLALLKPGDTFMGLSLAAGGHLTH 129 Query: 134 GAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRA 193 GA+P +SGKWFNA+QYGV LIDYD++E A +P LII G SAYPR +DF R RA Sbjct: 130 GARPTMSGKWFNAVQYGVRESDCLIDYDELEVKAIATRPKLIITGGSAYPRLIDFKRIRA 189 Query: 194 IADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAK 253 IADSVGA +MVDMAH AG++A G H NPVE A +VT+TTHKTLRGPRGG +LTN++++AK Sbjct: 190 IADSVGAAMMVDMAHFAGLVAGGVHPNPVEIADIVTTTTHKTLRGPRGGMILTNNQDVAK 249 Query: 254 KINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLV 313 K+NSAVFPGLQGGPLMHVIA KAVA GEAL D+F+ Y +++ANA+AL L G D+V Sbjct: 250 KVNSAVFPGLQGGPLMHVIAAKAVALGEALEDNFRQYARQMVANARALASALTERGYDIV 309 Query: 314 TGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGT 373 +GGTD HL+LVDLR KG+ G E+AL RAG+TCNKNGIPFDP P +TSGIRLGTPA T Sbjct: 310 SGGTDTHLILVDLRSKGVSGKDAEEALGRAGLTCNKNGIPFDPAPPAVTSGIRLGTPAAT 369 Query: 374 TRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424 +RGF AEF EVG LI V +AL T G+ E+R R + LC FPIY Sbjct: 370 SRGFREAEFNEVGALIANVLDALGTEQSGEQ--ERRARMSVHDLCAAFPIY 418 Lambda K H 0.318 0.136 0.391 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: 604 Number of extensions: 22 Number of successful extensions: 2 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: 424 Length of database: 422 Length adjustment: 32 Effective length of query: 392 Effective length of database: 390 Effective search space: 152880 Effective search space used: 152880 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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