Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate AO353_10530 AO353_10530 serine hydroxymethyltransferase
Query= BRENDA::A8GTI9 (420 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10530 Length = 432 Score = 467 bits (1202), Expect = e-136 Identities = 225/410 (54%), Positives = 302/410 (73%) Query: 7 NLHETDKEINEIIKHEKLRQSSVIELIASENFVSPAVLEAQGALLTNKYAEGYPSKRFYN 66 NL + D+++ I E+LRQ IELIA+ENFVS AVLEAQG++LTNK+AEGYP +R+Y Sbjct: 19 NLPQADRDVWRAIDTERLRQMHSIELIAAENFVSRAVLEAQGSVLTNKHAEGYPGRRYYA 78 Query: 67 GCEEVDKAENLAIERVKKLFNCKYANVQPHSGSQANQAVYLALLQPGDTVLGMSLDSGGH 126 GC VD+ EN+AIER K+LF C YANVQPHSGSQANQAV+LALL PGD +LG+ L +GGH Sbjct: 79 GCRNVDEIENIAIERAKRLFKCAYANVQPHSGSQANQAVFLALLAPGDKILGLDLKAGGH 138 Query: 127 LTHGAAPNMSGKWFNAVSYSVNKETYLIDYDEIERLADLHKPKLLIAGFSAYPRNIDFAK 186 L+HGA NMSG+WF A+SY V+ T+ +D D++ER+A +P+L+I G SAY R +DFA+ Sbjct: 139 LSHGATFNMSGRWFQALSYGVHPVTHRVDMDQVERIARQERPRLIIVGASAYSRTLDFAR 198 Query: 187 FREIVDKVGAYFMADIAHIAGLVATGEHQSPIPYAHAVTSTTHKTLRGPRGGLILSNDEE 246 FR I D+V A+ MADIAH++GLVA G + SP+P+AH T+TTH TLRGPRGG++L N++ Sbjct: 199 FRSIADEVDAFLMADIAHVSGLVAGGAYPSPVPFAHVTTTTTHTTLRGPRGGMVLCNEQA 258 Query: 247 IGHKINSALFPGLQGGPLMHIIAAKAVAFLENLQPEYKSYIQQVISNAKALASSLQERGY 306 I KIN+A+FPGLQ PLMHIIAAKAVA E LQP + +Y V++NA+AL L E G Sbjct: 259 IAQKINAAVFPGLQCAPLMHIIAAKAVALGEALQPSFSTYAHAVVANAQALCGRLAEGGL 318 Query: 307 DILTGGTDNHIVLVDLRKDGITGKLAANSLDRAGITCNKNAIPFDETSPFITSGIRLGTP 366 I++GGTD H+ ++DLR G+ G +A ++L++ GIT NKN +P DE P +TSGIRLG+ Sbjct: 319 SIVSGGTDCHLGVIDLRPWGLAGDVAEHALEQIGITVNKNTVPNDEARPAVTSGIRLGSA 378 Query: 367 ACTTRGFKEKDFVLVGHMVADILDGLKNNEDNSALEQQVLNEVTKLIELF 416 ACT+RG +F +G M+ +L G+++ + E+ + V L + F Sbjct: 379 ACTSRGMGADEFREIGDMILALLGGVRSGTIDCRTERSIREGVADLTKRF 428 Lambda K H 0.317 0.135 0.387 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: 522 Number of extensions: 20 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: 420 Length of database: 432 Length adjustment: 32 Effective length of query: 388 Effective length of database: 400 Effective search space: 155200 Effective search space used: 155200 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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