Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_012169792.1 AZC_RS06490 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >NCBI__GCF_000010525.1:WP_012169792.1 Length = 437 Score = 630 bits (1626), Expect = 0.0 Identities = 311/428 (72%), Positives = 359/428 (83%) Query: 6 AAGTASTSRFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTN 65 A+ +A +RFF + ++E DP+I +A+ E GRQ+ EIELIASENIVS+AVL+A GSVLTN Sbjct: 9 ASASAEMNRFFSASLAEVDPEIAAAVSAELGRQREEIELIASENIVSRAVLEAQGSVLTN 68 Query: 66 KYAEGYPGKRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPG 125 KYAEGYPGKRYYGGCQ+VD+ E++AIDRAKKLF C FANVQPNSGSQANQGVF L QPG Sbjct: 69 KYAEGYPGKRYYGGCQFVDVAENLAIDRAKKLFGCAFANVQPNSGSQANQGVFFTLMQPG 128 Query: 126 DTILGLSLAAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIA 185 DT LGL+LAAGGHLTHG+PVN SGKWF AV Y V+ D ID D V +LA +HKP++I+A Sbjct: 129 DTFLGLNLAAGGHLTHGSPVNMSGKWFNAVAYGVREDDQRIDYDVVAQLADQHKPKVIVA 188 Query: 186 GGSAYPRKIDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLR 245 GGSAYPR IDFA R IAD VGA +VDMAHFAGLVA G PSPFPHAHVVTTTTHKTLR Sbjct: 189 GGSAYPRVIDFARMRQIADSVGAKLMVDMAHFAGLVAGGAHPSPFPHAHVVTTTTHKTLR 248 Query: 246 GPRGGMILTNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDN 305 GPRGGMILTND ++AKK+NSAIFPGIQGGPLMHVIA KAVAFGEALRP+FKVY K V++N Sbjct: 249 GPRGGMILTNDEELAKKLNSAIFPGIQGGPLMHVIAAKAVAFGEALRPEFKVYAKNVVEN 308 Query: 306 ARALGEVLVQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPE 365 ARAL E L +GF +VS GTDTHL+LVDLRPK+LTG +E ALGRA+ITCNKNGIPFDPE Sbjct: 309 ARALAENLRGHGFDIVSDGTDTHLMLVDLRPKRLTGKISENALGRAHITCNKNGIPFDPE 368 Query: 366 KPMVTSGIRLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIA 425 KP VTSG+RLG+PAGTTRGFGVAEFQ+IG +I+EVLD +++ G + VE AV+ K + Sbjct: 369 KPAVTSGVRLGTPAGTTRGFGVAEFQQIGDMIAEVLDVLSQKGVAEDSLVEEAVRGKVKS 428 Query: 426 LCDRFPIY 433 L RFPIY Sbjct: 429 LLARFPIY 436 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: 605 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: 437 Length adjustment: 32 Effective length of query: 402 Effective length of database: 405 Effective search space: 162810 Effective search space used: 162810 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