Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate GFF3561 PGA1_c36150 phosphoserine aminotransferase SerC
Query= metacyc::MONOMER-15918 (370 letters) >FitnessBrowser__Phaeo:GFF3561 Length = 384 Score = 458 bits (1179), Expect = e-133 Identities = 227/372 (61%), Positives = 268/372 (72%), Gaps = 10/372 (2%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 +P P NP FSSGPCAK P + + +L P GRSHR+ GK+KL AI+ TR++LG+P Sbjct: 5 QPATRPGNPRFSSGPCAKPPAFDLTKLAGAPLGRSHRAAIGKDKLLAAIEGTREILGVPA 64 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 Y +GIVPASDTGA EM +W++LG RG ++L WESF GW TD+ KQLKL D V A+Y Sbjct: 65 GYRIGIVPASDTGAVEMAMWNLLGARGAEMLAWESFGAGWVTDVVKQLKL-DAVVKTADY 123 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G+L DL VDF NDVVF WNGTTSGV+VPN DWIP DR G+T+CDATSA FA D+P+ KL Sbjct: 124 GELVDLASVDFNNDVVFTWNGTTSGVRVPNGDWIPADRAGLTICDATSAAFAQDLPWDKL 183 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241 DV TFSWQKVLGGE AHGM+ILSPRAV+RLESYTPAWPLPKIFRLTKGGKL IF G+T Sbjct: 184 DVTTFSWQKVLGGEAAHGMIILSPRAVERLESYTPAWPLPKIFRLTKGGKLIDGIFKGAT 243 Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPSMLA ED+L L WA SVGGL L R + N F A WI LA RS Sbjct: 244 INTPSMLAVEDYLLALDWARSVGGLDGLKGRADANAQAIFNFCANRPWIANLATDPATRS 303 Query: 302 STSVCFKVDLSDEKL-------KELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKED 354 +TSVC K +D ++ K + K LE E +A DIG+YRDAP+GLRIWCG TVE D Sbjct: 304 NTSVCLK--FTDPRIQDGATFAKAIAKRLEAENIALDIGAYRDAPAGLRIWCGGTVETSD 361 Query: 355 LECLCEWIEWAY 366 +E + W+EWA+ Sbjct: 362 IEAMLPWLEWAF 373 Lambda K H 0.319 0.136 0.430 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: 488 Number of extensions: 17 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: 370 Length of database: 384 Length adjustment: 30 Effective length of query: 340 Effective length of database: 354 Effective search space: 120360 Effective search space used: 120360 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 Sep 17 2021. The underlying query database was built on Sep 17 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