Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 (characterized)
to candidate WP_072905509.1 BUB13_RS03165 serine hydroxymethyltransferase
Query= SwissProt::P39148 (415 letters) >NCBI__GCF_900142125.1:WP_072905509.1 Length = 417 Score = 551 bits (1421), Expect = e-161 Identities = 277/409 (67%), Positives = 317/409 (77%) Query: 2 KHLPAQDEQVFNAIKNERERQQTKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRYY 61 K+L A D ++ N I E ERQ+ +E IASENFVSEAV+EAQGSVLTNKYAEGYPGKRYY Sbjct: 4 KNLVAADAEIANIIDEETERQEYNLEFIASENFVSEAVLEAQGSVLTNKYAEGYPGKRYY 63 Query: 62 GGCEHVDVVEDIARDRAKEIFGAEHVNVQPHSGAQANMAVYFTILEQGDTVLGMNLSHGG 121 GGCE VD E +A DRAKE+FGAEH NVQPHSG+QANMAVY + E GDTVLGMNL+HGG Sbjct: 64 GGCEVVDKAEQLAIDRAKELFGAEHANVQPHSGSQANMAVYMAVCEPGDTVLGMNLAHGG 123 Query: 122 HLTHGSPVNFSGVQYNFVEYGVDKETQYIDYDDVREKALAHKPKLIVAGASAYPRTIDFK 181 HLTHGSPVNFSG YN V YGV +ET IDY++V A HKPKLIV GASAY R +DF Sbjct: 124 HLTHGSPVNFSGKLYNIVPYGVKEETGTIDYEEVERLAKEHKPKLIVVGASAYTRELDFP 183 Query: 182 KFREIADEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCREE 241 FR IADEVGA MVDMAHIAGLVAAG+HPNPVPYA+FVTTTTHKTLRGPRGGMILC EE Sbjct: 184 AFRRIADEVGAVVMVDMAHIAGLVAAGVHPNPVPYAEFVTTTTHKTLRGPRGGMILCTEE 243 Query: 242 FGKKIDKSIFPGIQGGPLMHVIAAKAVSFGEVLQDDFKTYAQNVISNAKRLAEALTKEGI 301 + KK++ +IFPGIQGGPLMHVIAAKAV+F E L +FK YAQ V+ NA+ LA L +G Sbjct: 244 WSKKLNSNIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYAQQVVKNAQTLASELVAKGY 303 Query: 302 QLVSGGTDNHLILVDLRSLGLTGKVAEHVLDEIGITSNKNAIPYDPEKPFVTSGIRLGTA 361 +LVSGGTDNHL+L+D LTGKVAE VL+E GIT NKNA+P+D PFVTSGIR+GT Sbjct: 304 KLVSGGTDNHLMLMDFTGTDLTGKVAEAVLEEAGITVNKNAVPFDTRSPFVTSGIRIGTP 363 Query: 362 AVTSRGFDGDALEEVGAIIALALKNHEDEGKLEEARQRVAALTDKFPLY 410 A TSRG + +V I A KN E++ +L + R V L +FPLY Sbjct: 364 ATTSRGLKEPEMVKVADWIDRAFKNAENKEELAKIRAEVKELCKQFPLY 412 Lambda K H 0.317 0.136 0.388 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: 598 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: 415 Length of database: 417 Length adjustment: 31 Effective length of query: 384 Effective length of database: 386 Effective search space: 148224 Effective search space used: 148224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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