Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate AMB_RS11815 AMB_RS11815 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__Magneto:AMB_RS11815 Length = 427 Score = 629 bits (1622), Expect = 0.0 Identities = 310/433 (71%), Positives = 361/433 (83%), Gaps = 7/433 (1%) Query: 1 MSSAPAAGTASTSRFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAG 60 MSSAP T FF++ +SE DP++F+AI +E RQQ +IELIASENIVS+AVL+A G Sbjct: 1 MSSAP------TDAFFRTPLSERDPEVFAAITQELKRQQDQIELIASENIVSRAVLEAQG 54 Query: 61 SVLTNKYAEGYPGKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNA 120 SV+TNKYAEGYPGKRYYGGC++VDI E +AI RA ++F C +ANVQP+SGSQANQGVF A Sbjct: 55 SVMTNKYAEGYPGKRYYGGCEFVDIAESLAISRACQIFGCSYANVQPSSGSQANQGVFMA 114 Query: 121 LAQPGDTILGLSLAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKP 180 L QPGDTI+G+SLAAGGHLTHGA NQSGKWFKAV Y V+ ID EV +LA+ H+P Sbjct: 115 LLQPGDTIMGMSLAAGGHLTHGAAPNQSGKWFKAVQYGVRQQDSQIDFAEVEELARTHRP 174 Query: 181 RIIIAGGSAYPRKIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTT 240 ++IIAGGSAYPR IDFA FR IADEVGA F+VDMAHFAGLVA G+ P+P PHAHVVTTTT Sbjct: 175 KLIIAGGSAYPRTIDFARFRKIADEVGAFFMVDMAHFAGLVAGGVYPNPLPHAHVVTTTT 234 Query: 241 HKTLRGPRGGMILTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIK 300 HKTLRGPRGGMIL+NDADI KKINSAIFPGIQGGPLMHVIAGKAVAFGEAL+P+FK+Y K Sbjct: 235 HKTLRGPRGGMILSNDADIGKKINSAIFPGIQGGPLMHVIAGKAVAFGEALKPEFKLYAK 294 Query: 301 QVMDNARALGEVLVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGI 360 QV+DNARAL + LV+ G +VSGGTD+HL+LVDLRPKKLTG AE +L A +TCNKNGI Sbjct: 295 QVVDNARALADTLVRRGLDIVSGGTDSHLMLVDLRPKKLTGKAAEASLEHAGMTCNKNGI 354 Query: 361 PFDPEKPMVTSGIRLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVK 420 PFDPEKP +TSG+RLG+PA TTRGFGV EF+++G LI +VLDG+A N ED N A EA + Sbjct: 355 PFDPEKPTITSGVRLGTPAATTRGFGVEEFKKVGELIGDVLDGLAANPED-NSAAEARAR 413 Query: 421 AKAIALCDRFPIY 433 A+ LC RFPIY Sbjct: 414 AEVAELCRRFPIY 426 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: 616 Number of extensions: 18 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: 427 Length adjustment: 32 Effective length of query: 402 Effective length of database: 395 Effective search space: 158790 Effective search space used: 158790 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