Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate Dsui_2254 Dsui_2254 glycine/serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__PS:Dsui_2254 Length = 433 Score = 542 bits (1397), Expect = e-159 Identities = 272/409 (66%), Positives = 322/409 (78%) Query: 24 DPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGKRYYGGCQYV 83 DP+ + E+ RQ+H IELIASENIVS+AVL+ GSVLTNKYAEGYPG+RYYGGC V Sbjct: 23 DPEAARYVAAEYARQRHSIELIASENIVSRAVLEMQGSVLTNKYAEGYPGRRYYGGCGPV 82 Query: 84 DIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLAAGGHLTHGA 143 D VE +AI RAK LF C +ANVQP+SGSQANQ V+ AL QPGDTILGL LAAGGHLTHGA Sbjct: 83 DGVEALAIARAKGLFGCAYANVQPHSGSQANQAVYLALLQPGDTILGLGLAAGGHLTHGA 142 Query: 144 PVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKIDFAAFRAIA 203 P+NQSGKWF+ V Y V+ D H IDM +V +LA E++P++IIAGGSAY R +DFA FR IA Sbjct: 143 PMNQSGKWFRGVAYGVRADDHRIDMAQVEQLAYEYRPKLIIAGGSAYSRILDFAEFRRIA 202 Query: 204 DEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILTNDADIAKKI 263 D VGA LVDMAHFAGLVA G PSP P+A VVT+TTHKTLRGPRGG+IL+NDA + K I Sbjct: 203 DRVGARLLVDMAHFAGLVAGGAHPSPLPYADVVTSTTHKTLRGPRGGLILSNDAALGKAI 262 Query: 264 NSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLVQNGFALVSG 323 +SA+FPG+QGGPLMHVI KAVAFGEAL+P+F+ Y +V++NA+AL + L G +VSG Sbjct: 263 DSAVFPGLQGGPLMHVIGAKAVAFGEALQPEFRSYAARVVENAQALADALAAGGLRIVSG 322 Query: 324 GTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIRLGSPAGTTR 383 GTDTHL + DLRP LTG AEKAL R IT NKN IP DP+KPMVTSGIR+GSPAGT+R Sbjct: 323 GTDTHLAVADLRPLNLTGNVAEKALERVGITLNKNAIPHDPQKPMVTSGIRVGSPAGTSR 382 Query: 384 GFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPI 432 GF AEF+ IG LI +L+ +A N E + AV AAV+A+ LC RFP+ Sbjct: 383 GFRTAEFRLIGGLIVHLLEALAANPEAPDPAVAAAVRAQVAELCRRFPL 431 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: 621 Number of extensions: 21 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: 433 Length adjustment: 32 Effective length of query: 402 Effective length of database: 401 Effective search space: 161202 Effective search space used: 161202 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