Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate 3608721 Dshi_2113 Glycine hydroxymethyltransferase (RefSeq)
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__Dino:3608721 Length = 424 Score = 560 bits (1442), Expect = e-164 Identities = 284/412 (68%), Positives = 324/412 (78%), Gaps = 1/412 (0%) Query: 23 TDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGKRYYGGCQY 82 +D I AI E RQQ +IELIASENIVS VL A GSVLTNKYAEGYPG+RYYGGC++ Sbjct: 11 SDTAIAEAIGHELDRQQTQIELIASENIVSVDVLRAQGSVLTNKYAEGYPGRRYYGGCEH 70 Query: 83 VDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLAAGGHLTHG 142 VD VE IAIDR +LF FANVQ +SG+QANQ VF AL +PGD I+GL LA GGHLTHG Sbjct: 71 VDTVEQIAIDRVCELFGSRFANVQAHSGAQANQAVFLALLKPGDRIMGLDLAHGGHLTHG 130 Query: 143 APVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKIDFAAFRAI 202 +PV SGKWF V Y V D HLIDMD VRK+A + KP++I+AG SAYPR +DFAAFRAI Sbjct: 131 SPVTMSGKWFDVVSYEVSRDDHLIDMDNVRKVALDTKPKLIVAGASAYPRHMDFAAFRAI 190 Query: 203 ADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILTNDADIAKK 262 ADEVGA +VDMAH+AGL+AAG P P PHAHVVT+TTHKTLRGPRGG+ILTND +AKK Sbjct: 191 ADEVGAWLMVDMAHYAGLIAAGEYPDPVPHAHVVTSTTHKTLRGPRGGIILTNDEALAKK 250 Query: 263 INSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLVQNGFALVS 322 NSA+FPG QGGPLMHVIA KAVAFGEAL P FK Y K V+ NARAL EVLV G +VS Sbjct: 251 FNSAVFPGNQGGPLMHVIAAKAVAFGEALEPSFKQYAKDVIANARALSEVLVAGGLGVVS 310 Query: 323 GGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIRLGSPAGTT 382 GGTD H+VLVDLRPK +TG AE AL RA +TCNKN IPFDPEKP VTSG+RLG+ AGTT Sbjct: 311 GGTDCHMVLVDLRPKGVTGKAAENALERAGLTCNKNAIPFDPEKPFVTSGVRLGTSAGTT 370 Query: 383 RGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPIYA 434 RGFG AEF+++G L+ V+D +A+N E G+ AVEAAV + ALC PIYA Sbjct: 371 RGFGEAEFRKVGALVLRVIDALAENAE-GDAAVEAAVLEEVRALCAAHPIYA 421 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: 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: 434 Length of database: 424 Length adjustment: 32 Effective length of query: 402 Effective length of database: 392 Effective search space: 157584 Effective search space used: 157584 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