Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Pf6N2E2_5082 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= BRENDA::L7Y8B0 (417 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5082 Length = 417 Score = 665 bits (1715), Expect = 0.0 Identities = 333/416 (80%), Positives = 368/416 (88%), Gaps = 1/416 (0%) Query: 1 MFSKQDQIQGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMQAQGSGLTNKYAEGYP 60 MFS+ I YD L AAM E QRQE+HIELIASENYTS VM+AQGS LTNKYAEGYP Sbjct: 1 MFSRDLTIAKYDADLFAAMEQEAQRQEEHIELIASENYTSPAVMEAQGSVLTNKYAEGYP 60 Query: 61 GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANGAVYLALVQAGDTILGMS 120 GKRYYGGCE+VD VE LAI+RAKQLFGADYANVQPH+GS AN AVYLAL+ AGDTILGMS Sbjct: 61 GKRYYGGCEYVDVVEQLAIDRAKQLFGADYANVQPHAGSQANSAVYLALLSAGDTILGMS 120 Query: 121 LAHGGHLTHGAKVSSSGKLYNAVQYGIDTNTGLIDYDEVERLAVEHKPKMIVAGFSAYSK 180 LAHGGHLTHGA VSSSGKLYNAVQYGID N GLIDYDEVERLA+EHKPKMIVAGFSAYS+ Sbjct: 121 LAHGGHLTHGASVSSSGKLYNAVQYGIDGN-GLIDYDEVERLALEHKPKMIVAGFSAYSQ 179 Query: 181 TLDFPRFRAIADKVGALLFVDMAHVAGLVAAGLYPNPIPFADVVTTTTHKTLRGPRGGLI 240 LDFPRFR IADKVGA LFVDMAHVAGLVAAG+YPNP+PFADVVTTTTHKTLRGPRGGLI Sbjct: 180 VLDFPRFREIADKVGAYLFVDMAHVAGLVAAGVYPNPVPFADVVTTTTHKTLRGPRGGLI 239 Query: 241 LAKANEEIEKKLNAAVFPGAQGGPLMHVIAAKAVCFKEALEPEFKAYQQQVIENAQAMAQ 300 LA+AN +IEK+LN+AVFPGAQGGPL HVIAAKA+CFKEAL+PEFKAYQQQV++NA+AMA Sbjct: 240 LARANADIEKRLNSAVFPGAQGGPLEHVIAAKAICFKEALQPEFKAYQQQVVKNAKAMAG 299 Query: 301 VFVDRGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGCAHITVNKNAVPNDPQSPFVTS 360 VF++RG+DVVSGGT+NHLFL+SLI+Q ++GKDADAALG A ITVNKN+VPNDP+SPFVTS Sbjct: 300 VFIERGFDVVSGGTENHLFLLSLIKQEISGKDADAALGKAFITVNKNSVPNDPRSPFVTS 359 Query: 361 GLRIGTPAVTTRGFKVAQCVALAGWICDILDNLGDADVEADVAKNVAALCADFPVY 416 GLR GTPAVTTRGFK A+C LAGWICDIL +L + V V + V A+C PVY Sbjct: 360 GLRFGTPAVTTRGFKEAECKELAGWICDILADLNNEAVIDAVREKVKAICKKLPVY 415 Lambda K H 0.318 0.134 0.390 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: 685 Number of extensions: 20 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: 417 Length of database: 417 Length adjustment: 31 Effective length of query: 386 Effective length of database: 386 Effective search space: 148996 Effective search space used: 148996 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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