Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate GFF1172 PGA1_c11870 serine hydroxymethyltransferase GlyA
Query= SwissProt::Q3JGP5 (424 letters) >FitnessBrowser__Phaeo:GFF1172 Length = 432 Score = 575 bits (1481), Expect = e-168 Identities = 285/419 (68%), Positives = 337/419 (80%), Gaps = 1/419 (0%) Query: 7 FFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGK 66 FF+QSLAERD + G+I EL RQ+ ++ELIASENIVS AV++AQG+VLTNKYAEGYPG+ Sbjct: 11 FFTQSLAERDPELFGSITDELGRQRDEIELIASENIVSAAVMEAQGTVLTNKYAEGYPGR 70 Query: 67 RYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLD 126 RYYGGC++ D E LAI+R K+LF+ ANVQP+SG+QAN V AL KPGDT+LGM L Sbjct: 71 RYYGGCQYVDVAENLAIDRAKKLFDCEFANVQPNSGSQANQGVFQALIKPGDTILGMDLA 130 Query: 127 AGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKL 186 +GGHLTHGA+P SGKWFNA+ YGV + LIDYDQ+EALA +H+P LIIAG SA PR + Sbjct: 131 SGGHLTHGARPNQSGKWFNAVHYGVREEDCLIDYDQIEALAVEHQPKLIIAGGSAIPRVI 190 Query: 187 DFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLT 246 DFARFR IAD VGA L VDMAH AG++AAG H +P HAHV T+TTHKTLRGPRGG +LT Sbjct: 191 DFARFREIADKVGAYLHVDMAHFAGLVAAGEHPSPFPHAHVATTTTHKTLRGPRGGMILT 250 Query: 247 NDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLK 306 ND +IAKK+NSA+FPG+QGGPLMHVIA KAVAFGEAL +FK Y +V ANA AL D L Sbjct: 251 NDADIAKKVNSAIFPGIQGGPLMHVIAAKAVAFGEALRPEFKDYQKQVRANAVALSDQLI 310 Query: 307 AGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIR 366 GG+D+VTGGTD H++LVDLRPKG+ G V++AL RA IT NKNGIPFDPEKPT+TSGIR Sbjct: 311 KGGLDIVTGGTDTHVMLVDLRPKGVTGNIVDKALGRAHITTNKNGIPFDPEKPTVTSGIR 370 Query: 367 LGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHAT-EQRVRREIFALCERFPIY 424 LGTPAGTTRGFG AEFRE+ LI+EV + L N E +AT E VR ++ ALC RFP+Y Sbjct: 371 LGTPAGTTRGFGEAEFREIADLIIEVVDGLAANGEDGNATVEASVREKVAALCARFPLY 429 Lambda K H 0.318 0.136 0.391 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: 651 Number of extensions: 29 Number of successful extensions: 3 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: 424 Length of database: 432 Length adjustment: 32 Effective length of query: 392 Effective length of database: 400 Effective search space: 156800 Effective search space used: 156800 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 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