Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_015933126.1 MNOD_RS32140 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_000022085.1:WP_015933126.1 Length = 390 Score = 444 bits (1141), Expect = e-129 Identities = 223/376 (59%), Positives = 270/376 (71%), Gaps = 12/376 (3%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 +P P+ P FSSGPCAK PG++ L D GRSHR+K GK KL EAI TR +L +PD Sbjct: 4 RPDARPRAPFFSSGPCAKRPGWTPAALSDAALGRSHRAKLGKTKLREAIDLTRAVLEVPD 63 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 DY +GIVPASDTGA EM +WS+LG R V++L WESF +GW TD KQL+L D RV A Y Sbjct: 64 DYRIGIVPASDTGAVEMAMWSLLGPRPVEMLAWESFGEGWVTDAVKQLRL-DARVTTAPY 122 Query: 122 GKLPDLKKVDFK-NDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHK 180 G+LPDL +D K +DVVF WNGTTSGV+VP+ADWI DREGV +CDATSA FA ++ + K Sbjct: 123 GQLPDLSGIDTKQHDVVFTWNGTTSGVRVPDADWIAADREGVVICDATSAAFAQNLDWGK 182 Query: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGS 240 LD +TFSWQKVLGGE AHGMLILSPRAV RLESYTP+WP+PKIFR+TKGGKL + IF G Sbjct: 183 LDAVTFSWQKVLGGEAAHGMLILSPRAVARLESYTPSWPMPKIFRMTKGGKLIEGIFQGE 242 Query: 241 TINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIR 300 TINTPSMLA ED++ L+WAE +GGL L R + N V +VA+ WI LA Sbjct: 243 TINTPSMLAVEDYIDALRWAEGLGGLPALRARADANAKVVADWVARTPWIANLAADPRHA 302 Query: 301 SSTSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATV 350 S+TSVC + + K + +LE+E VA+DIG+YRDAP+GLRIWCGATV Sbjct: 303 SNTSVCLVIADPEVTGRGPEAVAALAKGIAASLEREGVAFDIGAYRDAPAGLRIWCGATV 362 Query: 351 EKEDLECLCEWIEWAY 366 E DLE L W++WA+ Sbjct: 363 EAADLEALTPWLDWAF 378 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: 493 Number of extensions: 20 Number of successful extensions: 4 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: 390 Length adjustment: 30 Effective length of query: 340 Effective length of database: 360 Effective search space: 122400 Effective search space used: 122400 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 24 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