Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate CCNA_01419 CCNA_01419 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__Caulo:CCNA_01419 Length = 428 Score = 576 bits (1485), Expect = e-169 Identities = 281/421 (66%), Positives = 337/421 (80%) Query: 13 SRFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYP 72 S FF + ++ D DIF I +E GRQQ++IELIASENIVS+AVL+A GS+LTNKYAEGYP Sbjct: 7 SAFFGADLATADRDIFDRIGRELGRQQNQIELIASENIVSKAVLEAQGSILTNKYAEGYP 66 Query: 73 GKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLS 132 GKRYYGGC+YVD +E IAI+RAK LF FANVQP+SGSQANQ VF AL QPGDT LG+ Sbjct: 67 GKRYYGGCEYVDEIETIAIERAKALFGAGFANVQPHSGSQANQAVFMALLQPGDTFLGMD 126 Query: 133 LAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPR 192 LAAGGHLTHG+P NQSGKWFK + Y V+ LID D V ++AQ KP++IIAGGSAY R Sbjct: 127 LAAGGHLTHGSPANQSGKWFKPISYSVRQQDQLIDYDGVAEVAQREKPKLIIAGGSAYSR 186 Query: 193 KIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMI 252 +IDFA FR IAD +GA +VDMAH+AGL+A G +P PHAH+VTTTTHKTLRGPRGG++ Sbjct: 187 EIDFAKFREIADSIGAYLMVDMAHYAGLIAGGAYANPIPHAHIVTTTTHKTLRGPRGGLV 246 Query: 253 LTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEV 312 LTND I KK+NSA+FPG+QGGPL HVIA KAVAFGEAL+P FK Y +QV+ NARAL E Sbjct: 247 LTNDEAIIKKVNSAVFPGLQGGPLEHVIAAKAVAFGEALQPSFKDYARQVVANARALAEA 306 Query: 313 LVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSG 372 L+++G +VSGGTD+HL+LVDLRPK +TG AE +L RA +TCNKNG+PFD +TSG Sbjct: 307 LLKSGVNIVSGGTDSHLMLVDLRPKGVTGRDAEHSLERAYMTCNKNGVPFDTAPFTITSG 366 Query: 373 IRLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPI 432 IRLG+PAGTTRGF AEF +G LI EV++G+A NG +GN AVEA V+ + +AL RFPI Sbjct: 367 IRLGTPAGTTRGFKEAEFTRVGELIGEVVNGLAVNGPEGNAAVEAKVREEVLALTGRFPI 426 Query: 433 Y 433 Y Sbjct: 427 Y 427 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: 587 Number of extensions: 16 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: 428 Length adjustment: 32 Effective length of query: 402 Effective length of database: 396 Effective search space: 159192 Effective search space used: 159192 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