Align Glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_029131711.1 A3GO_RS0100345 serine hydroxymethyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2685 (418 letters) >NCBI__GCF_000428045.1:WP_029131711.1 Length = 417 Score = 650 bits (1677), Expect = 0.0 Identities = 322/417 (77%), Positives = 356/417 (85%) Query: 1 MFSKHDQIKGYDDELLAAMNAEDARQEHHIELIASENYTSQRVMQAQGSGLTNKYAEGYP 60 MFSK QI GYDDEL A+ +E+ RQE HIELIASENYTS RVMQAQGS LTNKYAEGYP Sbjct: 1 MFSKDMQIGGYDDELWEAIQSEEVRQEEHIELIASENYTSPRVMQAQGSVLTNKYAEGYP 60 Query: 61 GKRYYGGCEHVDVVEQLAIDRARQLFGADYANVQPHSGSQANAAVYLALLQAGDTVLGMS 120 GKRYYGGCE+VD+ EQLAIDRA+ LFGADYANVQPHSGSQANAAVY+AL Q GDTVLGMS Sbjct: 61 GKRYYGGCEYVDIAEQLAIDRAKALFGADYANVQPHSGSQANAAVYMALCQPGDTVLGMS 120 Query: 121 LAHGGHLTHGAKVSFSGKLYNAVQYGIDTTTGLIDYDEVERLAVEHKPKMIIAGFSAYSK 180 LAHGGHLTHGAK +FSGKLYNAVQYG+D TG IDY EVERLA EHKPKMI+AGFSAYS+ Sbjct: 121 LAHGGHLTHGAKPNFSGKLYNAVQYGLDPATGEIDYAEVERLAGEHKPKMIVAGFSAYSR 180 Query: 181 TLDFPRFRQIADKVGAYFFVDMAHVAGLVATGLYPNPLPYADVVTTTTHKTLRGPRGGLI 240 +D+ RFR IAD+VGAYFFVDMAHVAGL+A GLYP+P+ ADV TTTTHKTLRGPRGGLI Sbjct: 181 VIDWQRFRAIADEVGAYFFVDMAHVAGLIAAGLYPSPVRIADVTTTTTHKTLRGPRGGLI 240 Query: 241 LAKANPELEKKLNAAVFPGGQGGPLMHVIAAKAVCFKEALEPAFKTYQSQVIRNAQAMAQ 300 LAKANPELEKKLN+ VFPG QGGPLMHVIAAKAV FKEA+EP FKTYQ QV+ NAQAMA Sbjct: 241 LAKANPELEKKLNSLVFPGTQGGPLMHVIAAKAVAFKEAMEPGFKTYQQQVMTNAQAMAS 300 Query: 301 VFIERGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGRAGITVNKNAVPNDPQSPFVTS 360 VFIERGYDVVSGGT++HLFLVS I+ GLTGKD DA LG A ITVN NAVPNDPQSPF+TS Sbjct: 301 VFIERGYDVVSGGTNDHLFLVSFIQAGLTGKDVDAWLGAANITVNMNAVPNDPQSPFITS 360 Query: 361 GLRIGTPAITSRGFKEAQSIALAGWICDILDHLGDADIEANVARQAAALCADFPVYR 417 G+R+GTPA+T+RG EA++ LAGW+CD++D GD V Q LC PVY+ Sbjct: 361 GIRVGTPALTTRGVGEAEAKELAGWMCDVIDSRGDQTAIDRVKVQVLDLCKRHPVYK 417 Lambda K H 0.319 0.135 0.395 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: 652 Number of extensions: 23 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: 418 Length of database: 417 Length adjustment: 32 Effective length of query: 386 Effective length of database: 385 Effective search space: 148610 Effective search space used: 148610 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: 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