Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate 3607407 Dshi_0821 Glycine hydroxymethyltransferase (RefSeq)
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__Dino:3607407 Length = 431 Score = 620 bits (1598), Expect = 0.0 Identities = 306/419 (73%), Positives = 348/419 (83%) Query: 15 FFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGK 74 FF ++ D ++F AI KE GRQ+ EIELIASENIVS AV++A GSVLTNKYAEGYPG+ Sbjct: 10 FFTESLATRDAELFGAITKELGRQRDEIELIASENIVSAAVMEAQGSVLTNKYAEGYPGR 69 Query: 75 RYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLA 134 RYYGGCQYVDI E++AIDRA++LF C FANVQPNSGSQANQGVF AL QPGDTILG+SL Sbjct: 70 RYYGGCQYVDIAEELAIDRARQLFGCAFANVQPNSGSQANQGVFTALLQPGDTILGMSLD 129 Query: 135 AGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKI 194 AGGHLTHGA NQSGKWF AV Y V+ D+ +D D++ LA EHKP++IIAGGSA PR I Sbjct: 130 AGGHLTHGAKPNQSGKWFNAVQYGVRQDTLDVDYDQIAALAAEHKPKMIIAGGSAIPRII 189 Query: 195 DFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILT 254 DFA R IAD VGA LVDMAHFAGLVAAG PSPFPHAHV TTTTHKTLRGPRGGMILT Sbjct: 190 DFARIREIADSVGAWVLVDMAHFAGLVAAGHYPSPFPHAHVATTTTHKTLRGPRGGMILT 249 Query: 255 NDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLV 314 +D +AKK NSAIFPGIQGGPLMHVIAGKAVAFGEALRP+FK Y QV++NA+AL + L+ Sbjct: 250 DDEALAKKFNSAIFPGIQGGPLMHVIAGKAVAFGEALRPEFKTYQAQVIENAQALADQLM 309 Query: 315 QNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIR 374 Q G +V+GGTDTH++LVDLRPK + G EKALGRA+ITCNKNGIPFD EKPM+TSGIR Sbjct: 310 QGGLDIVTGGTDTHVLLVDLRPKGVKGNATEKALGRAHITCNKNGIPFDTEKPMITSGIR 369 Query: 375 LGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPIY 433 LGSPAGTTRGFG EF++I I V+DG+A NGEDGN VEAAV+A+ + LC RFPIY Sbjct: 370 LGSPAGTTRGFGTPEFRQIADWIVRVVDGLAANGEDGNAEVEAAVRAEVLELCGRFPIY 428 Lambda K H 0.319 0.136 0.396 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: 631 Number of extensions: 22 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: 434 Length of database: 431 Length adjustment: 32 Effective length of query: 402 Effective length of database: 399 Effective search space: 160398 Effective search space used: 160398 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: 51 (24.3 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