Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate GFF1172 PGA1_c11870 serine hydroxymethyltransferase GlyA
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__Phaeo:GFF1172 Length = 432 Score = 634 bits (1635), Expect = 0.0 Identities = 315/428 (73%), Positives = 360/428 (84%), Gaps = 3/428 (0%) Query: 9 TASTSR---FFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTN 65 T +TSR FF ++E DP++F +I E GRQ+ EIELIASENIVS AV++A G+VLTN Sbjct: 2 TVTTSRDPGFFTQSLAERDPELFGSITDELGRQRDEIELIASENIVSAAVMEAQGTVLTN 61 Query: 66 KYAEGYPGKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPG 125 KYAEGYPG+RYYGGCQYVD+ E++AIDRAKKLF+CEFANVQPNSGSQANQGVF AL +PG Sbjct: 62 KYAEGYPGRRYYGGCQYVDVAENLAIDRAKKLFDCEFANVQPNSGSQANQGVFQALIKPG 121 Query: 126 DTILGLSLAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIA 185 DTILG+ LA+GGHLTHGA NQSGKWF AVHY V+ + LID D++ LA EH+P++IIA Sbjct: 122 DTILGMDLASGGHLTHGARPNQSGKWFNAVHYGVREEDCLIDYDQIEALAVEHQPKLIIA 181 Query: 186 GGSAYPRKIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLR 245 GGSA PR IDFA FR IAD+VGA VDMAHFAGLVAAG PSPFPHAHV TTTTHKTLR Sbjct: 182 GGSAIPRVIDFARFREIADKVGAYLHVDMAHFAGLVAAGEHPSPFPHAHVATTTTHKTLR 241 Query: 246 GPRGGMILTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDN 305 GPRGGMILTNDADIAKK+NSAIFPGIQGGPLMHVIA KAVAFGEALRP+FK Y KQV N Sbjct: 242 GPRGGMILTNDADIAKKVNSAIFPGIQGGPLMHVIAAKAVAFGEALRPEFKDYQKQVRAN 301 Query: 306 ARALGEVLVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPE 365 A AL + L++ G +V+GGTDTH++LVDLRPK +TG +KALGRA+IT NKNGIPFDPE Sbjct: 302 AVALSDQLIKGGLDIVTGGTDTHVMLVDLRPKGVTGNIVDKALGRAHITTNKNGIPFDPE 361 Query: 366 KPMVTSGIRLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIA 425 KP VTSGIRLG+PAGTTRGFG AEF+EI LI EV+DG+A NGEDGN VEA+V+ K A Sbjct: 362 KPTVTSGIRLGTPAGTTRGFGEAEFREIADLIIEVVDGLAANGEDGNATVEASVREKVAA 421 Query: 426 LCDRFPIY 433 LC RFP+Y Sbjct: 422 LCARFPLY 429 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: 642 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: 432 Length adjustment: 32 Effective length of query: 402 Effective length of database: 400 Effective search space: 160800 Effective search space used: 160800 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