Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate CCNA_03323 CCNA_03323 phosphoserine aminotransferase
Query= metacyc::MONOMER-15918 (370 letters) >FitnessBrowser__Caulo:CCNA_03323 Length = 396 Score = 461 bits (1187), Expect = e-134 Identities = 230/383 (60%), Positives = 275/383 (71%), Gaps = 15/383 (3%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 KP P P FSSGPCAK PG++ E L++ GRSHRSK GK +L AI +TR++L +P Sbjct: 7 KPAIRPARPEFSSGPCAKRPGWTPENLRNAVLGRSHRSKLGKARLKAAIDQTREVLEVPA 66 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 D+ +GIV SDTGA EM +WSMLG R V +L +ESF K W TD+TKQLKL D V A Y Sbjct: 67 DFLIGIVAGSDTGAVEMAMWSMLGARPVQLLAFESFGKDWVTDVTKQLKLPDVEVLSAPY 126 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G+LPD KVD D+VF WNGTTSGV+VPNAD+I DREG+T+CDATSA FA D+ + KL Sbjct: 127 GQLPDTSKVDPAKDLVFTWNGTTSGVRVPNADFISADREGITICDATSAAFAQDLDWTKL 186 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTK-----GGKLNKDI 236 DV+TFSWQK LGGEGAHG+LILSPRAV RLESYTPAWP+PK+FR+TK G K++ DI Sbjct: 187 DVVTFSWQKALGGEGAHGVLILSPRAVARLESYTPAWPMPKLFRMTKANKDGGNKVSLDI 246 Query: 237 FAGSTINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAET 296 F G+TINTPSML ED L LKWA S+GGL+ + R ++NL V +VAK W+ FLA T Sbjct: 247 FEGATINTPSMLCVEDALDALKWASSIGGLQAMQARADQNLKVLADWVAKTPWVDFLAAT 306 Query: 297 KEIRSSTSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWC 346 EIRS+TSVC KV D + K+L LEKE A DIG YRDAP+GLRIWC Sbjct: 307 PEIRSNTSVCLKVVDPAICALPEDAQADFAKKLASLLEKEGAALDIGGYRDAPAGLRIWC 366 Query: 347 GATVEKEDLECLCEWIEWAYNLV 369 GATVE DLE L W++WA+ V Sbjct: 367 GATVEASDLEALTPWLDWAFATV 389 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: 494 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: 396 Length adjustment: 30 Effective length of query: 340 Effective length of database: 366 Effective search space: 124440 Effective search space used: 124440 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