Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate 8502391 DvMF_3097 serine hydroxymethyltransferase (RefSeq)
Query= BRENDA::Q5HE87 (412 letters) >FitnessBrowser__Miya:8502391 Length = 412 Score = 522 bits (1345), Expect = e-153 Identities = 264/411 (64%), Positives = 306/411 (74%), Gaps = 1/411 (0%) Query: 1 MSYITKQDKVIAEAIEREFQRQNSNIELIASENFVSEAVMEAQGSVLTNKYAEGYPGRRY 60 M + QD + A+ E +RQ +ELIASENFVS AV +AQGSVLT+KYAEGYPG+RY Sbjct: 1 MDELLIQDPEVGRAVTLEIERQTGKLELIASENFVSAAVRQAQGSVLTHKYAEGYPGKRY 60 Query: 61 YGGCEFVDVTESIAIDRAKALFGAEHVNVQPHSGSQANMAVYLVALEMGDTVLGMNLSHG 120 YGGCEFVD+ E++AIDRAKA+FG + NVQPHSGSQANM VY L+ GDT+LGMNLSHG Sbjct: 61 YGGCEFVDIAENLAIDRAKAIFGCGYANVQPHSGSQANMGVYFACLKPGDTILGMNLSHG 120 Query: 121 GHLTHGAPVNFSGKFYNFVEYGVDKDTERINYDEVRKLALEHKPKLIVAGASAYSRTIDF 180 GHLTHG+PVNFSG+ YN V YGV K+T I+YDEV LA EHKP LIVAGASAY RTIDF Sbjct: 121 GHLTHGSPVNFSGRLYNVVFYGVKKETGYIDYDEVAALAREHKPTLIVAGASAYPRTIDF 180 Query: 181 KKFKEIADEVNAKLMVDMAHIAGLVAAGLHPNPVEYADFVTTTTHKTLRGPRGGMILCKE 240 +F+ IADEV AKLMVDMAHIAGLVA GLHP P+ A F TTTTHKTLRGPRGGMIL E Sbjct: 181 ARFRAIADEVGAKLMVDMAHIAGLVATGLHPTPIGQAHFTTTTTHKTLRGPRGGMILSDE 240 Query: 241 EYKKDIDKTIFPGIQGGPLEHVIAAKAVAFGEALENNFKTYQQQVVKNAKVLAEALINEG 300 + K ++ IFPGIQGGPL HVIAAKAVAFGEAL F YQQQVVKNA LA L G Sbjct: 241 DNAKTLNSQIFPGIQGGPLMHVIAAKAVAFGEALRPTFVDYQQQVVKNAARLAGCLTAAG 300 Query: 301 FRIVSGGTDNHLVAVDVKGSIGLTGKEAEETLDSVGITCNKNTIPFDQEKPFVTSGIRLG 360 + +VSGGTDNHL+ +D+ +TGK+AE LD G+T NKNT+PF+ PFVTSG+RLG Sbjct: 301 YDLVSGGTDNHLMLMDLTAK-DITGKDAEHALDKAGMTANKNTVPFETRSPFVTSGVRLG 359 Query: 361 TPAATTRGFDEKAFEEVAKIISLALKNSKDEEKLQQAKERVAKLTAEYPLY 411 TPA TTRG E E+VA I AL N +E +L V ++PL+ Sbjct: 360 TPALTTRGMKEAEMEKVAAWIVDALANVNNETRLAAISREVEVFARQFPLF 410 Lambda K H 0.315 0.133 0.372 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: 552 Number of extensions: 24 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: 412 Length of database: 412 Length adjustment: 31 Effective length of query: 381 Effective length of database: 381 Effective search space: 145161 Effective search space used: 145161 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 (21.6 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