Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_043879456.1 AZC_RS15745 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >NCBI__GCF_000010525.1:WP_043879456.1 Length = 424 Score = 592 bits (1525), Expect = e-174 Identities = 286/410 (69%), Positives = 341/410 (83%) Query: 24 DPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGKRYYGGCQYV 83 D +F AI +E GRQ+ +IELIASENIVS+AVL A GSVLTNKYAEG PGKRYYGGC++V Sbjct: 12 DRAVFDAIARELGRQRDQIELIASENIVSEAVLAAQGSVLTNKYAEGLPGKRYYGGCEHV 71 Query: 84 DIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLAAGGHLTHGA 143 D+VE+IAIDRAK+LF C FANVQP+SG+QAN V AL QPGDT+LG+SLAAGGHLTHGA Sbjct: 72 DVVEEIAIDRAKQLFGCGFANVQPHSGAQANAAVLMALLQPGDTLLGMSLAAGGHLTHGA 131 Query: 144 PVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKIDFAAFRAIA 203 P SGKWF AV Y V P++ LID DEV +LA H+P++IIAGGS+YPR IDFA FRAIA Sbjct: 132 PPTLSGKWFNAVGYGVSPETALIDYDEVERLAHAHRPKLIIAGGSSYPRIIDFARFRAIA 191 Query: 204 DEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILTNDADIAKKI 263 D VGA +VD AH+AGL+ AG PSPFPHAH+VTTTTHKTLRGPRGG+ILTND +AKK+ Sbjct: 192 DAVGAHLMVDAAHYAGLIVAGAYPSPFPHAHIVTTTTHKTLRGPRGGLILTNDEALAKKL 251 Query: 264 NSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLVQNGFALVSG 323 NSA+FPG+QGGPLMHVIA KAVAFGEAL+PDF+ Y QV+ NARAL L + G A+VSG Sbjct: 252 NSAVFPGLQGGPLMHVIAAKAVAFGEALQPDFRTYALQVVSNARALAARLAEKGAAIVSG 311 Query: 324 GTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIRLGSPAGTTR 383 GTD+H+VLVDLRP +TG AE AL RA +TCNKNGIPFDP+KP VTSGIRLG+PAGTTR Sbjct: 312 GTDSHMVLVDLRPFNVTGKAAEIALERAGLTCNKNGIPFDPQKPAVTSGIRLGTPAGTTR 371 Query: 384 GFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPIY 433 GFG+ EF+++G +I+EVL G+A++G++GN EA V+ + ALC RFP+Y Sbjct: 372 GFGLGEFEQVGDMIAEVLKGLAQSGDEGNSLTEARVRGEVEALCRRFPLY 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: 613 Number of extensions: 24 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: 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 Jul 25 2024. The underlying query database was built on Jul 25 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