Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF2236 Psest_2281 Phosphoserine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__psRCH2:GFF2236 Length = 366 Score = 312 bits (800), Expect = 8e-90 Identities = 164/361 (45%), Positives = 223/361 (61%), Gaps = 3/361 (0%) Query: 2 AQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLL 61 A+ +NF+SGPAMLPAEVL+Q + EL +W G+SV+E +F Q+ E E D R LL Sbjct: 9 AERYNFASGPAMLPAEVLEQIRDELPNWRNTGSSVLEQPFTSTDFKQLMAETEADLRALL 68 Query: 62 NVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDA 121 +P NY+VLF GG QF +PLN+L +ADY+++G+WA AI EA+++ NV A Sbjct: 69 TIPDNYRVLFMQGGASAQFGLLPLNLLQPGQSADYLESGHWARKAITEARRHSPVNVV-A 127 Query: 122 KVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILS 181 A+ P+ WQL A Y H NET +G+ + + P+ +V AD +S L+ Sbjct: 128 SGADQAFTALPPLDHWQLDPAAGYCHVTSNETGNGLQLQKFPELVVPLV--ADMTSDFLT 185 Query: 182 RPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTP 241 R + + R+G+IYA AQKN+G AGL IVI+R DLL P+ Y+ + S FNTP Sbjct: 186 RQLPLERFGLIYASAQKNLGIAGLCIVIIRNDLLRAPPPGLPTAFSYATQAEQQSRFNTP 245 Query: 242 PTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVP 301 PTFA Y++GL+ +W+ NGGV M QQK+ LLY +DNSD Y A+RS +NV Sbjct: 246 PTFAVYVTGLMLRWMGRNGGVPAMAAAAQQKSCLLYRCVDNSDLYLCPQRPADRSPINVC 305 Query: 302 FQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361 FQL L + FL E+ GL L+GH +GG+RAS+YN MPL GV L +FM +FER+H Sbjct: 306 FQLTKPGLTETFLTEAERNGLTNLRGHAAIGGIRASLYNPMPLSGVARLVEFMTDFERKH 365 Query: 362 G 362 G Sbjct: 366 G 366 Lambda K H 0.319 0.136 0.405 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: 370 Number of extensions: 14 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: 362 Length of database: 366 Length adjustment: 29 Effective length of query: 333 Effective length of database: 337 Effective search space: 112221 Effective search space used: 112221 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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