Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_013683772.1 ARCVE_RS05470 serine hydroxymethyltransferase
Query= BRENDA::Q58992 (429 letters) >NCBI__GCF_000194625.1:WP_013683772.1 Length = 434 Score = 498 bits (1283), Expect = e-145 Identities = 248/426 (58%), Positives = 316/426 (74%), Gaps = 6/426 (1%) Query: 1 MEYSDVPKFIRDVSIKQHEWMRESIKLIASENITSLAVREACATDFMHRYAEGLPGKRLY 60 +E+S+ + + + HE+ R+SI LIASEN+ SLAVR TDF HRYAEG GKR Y Sbjct: 2 LEHSEYYSKLVETLRQHHEFYRQSIPLIASENLASLAVRSMYLTDFGHRYAEGRVGKRFY 61 Query: 61 QGCKYIDEVETLCIELSKELFKAEHANVQPTSGVVANLAVFFAETKPGDKLMALSVPDGG 120 QGC+YID VE + I+L+KE+F AEHANVQP SGV AN+A FFA T PGDKLMALSVP GG Sbjct: 62 QGCQYIDVVEDMAIQLTKEIFNAEHANVQPISGVTANIAAFFALTSPGDKLMALSVPCGG 121 Query: 121 HISHWKVSAAGIRGLKVINHPFDPEEMNIDADAMVKKILEEKPKLILFGGSLFPFPHPVA 180 HISH + SAAGIRGL+V+++PFD + +N+D D K +EKPK+ + G SL FPHPV Sbjct: 122 HISHDRFSAAGIRGLEVLHYPFDMDNLNVDVDETRKVAEKEKPKVFVLGSSLILFPHPVK 181 Query: 181 DAYEAAQEVGAKIAYDGAHVLGLIAGKQFQDPLREGAEYLMGSTHKTFFGPQGGVILTTK 240 + E A E+GA++ YDG+HVLGLIAGKQFQDP++EGA+ + STHKTFFGPQ +IL Sbjct: 182 EIAEIAAEIGARVVYDGSHVLGLIAGKQFQDPVKEGADVITASTHKTFFGPQRAIILCKA 241 Query: 241 ENADKIDSHVFPGVVSNHHLHHKAGLAIALAEMLEFGEAYAKQVIKNAKALAQALYERGF 300 E A KID+ VFPGVVSNHHLH AG IA EMLEFGEAYA+Q+++NAK LA+ ++E GF Sbjct: 242 ELAKKIDNAVFPGVVSNHHLHSLAGYVIACLEMLEFGEAYARQIVRNAKRLAERMHELGF 301 Query: 301 NVLCEHKDFTESHQVIIDIESSPDIEFSASE-LAKMYEEANIILNKNLLPWDDVNNSDNP 359 NV+ EH FTESHQV +D+ EF + +AK++E NIILNKNLLPWDD+ + NP Sbjct: 302 NVVGEHLGFTESHQVAVDV-----TEFGGGDPVAKLFERINIILNKNLLPWDDLTKTKNP 356 Query: 360 SGIRLGTQECTRLGMKEKEMEEIAEFMKRIAIDKEKPEKVREDVKEFAKEYSTIHYSFDE 419 SGIR+G QE TRLGMKE EME++AE M K+ +K+R++V E KE++TI Y+F+E Sbjct: 357 SGIRIGVQEITRLGMKEGEMEKLAEIMWDAVNGKKSEDKLRQEVIELKKEFNTIKYAFEE 416 Query: 420 GDGFKY 425 + + + Sbjct: 417 TEAYTF 422 Lambda K H 0.318 0.135 0.394 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: 538 Number of extensions: 19 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: 429 Length of database: 434 Length adjustment: 32 Effective length of query: 397 Effective length of database: 402 Effective search space: 159594 Effective search space used: 159594 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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