Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 3609943 Dshi_3325 aminotransferase class V (RefSeq)
Query= BRENDA::P74281 (384 letters) >FitnessBrowser__Dino:3609943 Length = 422 Score = 252 bits (643), Expect = 2e-71 Identities = 139/364 (38%), Positives = 210/364 (57%), Gaps = 3/364 (0%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 + L IPGP+ VP+++L A++ I HR DF+ + + +K + +T+ +V + +SG Sbjct: 33 RHFLQIPGPSAVPDRILRAISMQTIDHRGPDFADVGQKALKGMKTIFRTDQNVFIFPSSG 92 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 TGA EA+++N +SPGD VL+ G F W K+AK GL I+ +W DP + Sbjct: 93 TGAWEAALVNTMSPGDTVLMYETGHFATLWQKMAKKIGLNPVFIEGDWRGGADPQAIEDA 152 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHG-GALMIVDAVTSLGATPVAIDD 182 L D+D IKA+ + H+ETSTG ++ +A + AA A G AL++VD+++ L + P D Sbjct: 153 LRKDTDHEIKAVCVVHNETSTGSVSPIAEVRAAMDATGHPALLMVDSISGLASVPFEFDA 212 Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFT 242 G+DV SGSQKG M+PPGL F +VS KA + ++A + R Y D P+T Sbjct: 213 WGVDVCVSGSQKGLMLPPGLSFNAVSDKALEVAKSAKMQRSYWDWLDMVGPNATGYFPYT 272 Query: 243 PPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLP-LFAPDNAASNAITA 301 P NL+YGL ++ M+ EGL+ +F RH+RH ATR A++A L L A S +TA Sbjct: 273 PGTNLLYGLNEAVDMLHEEGLENVFERHRRHGAATRAAVRAWGLEVLCARQGQESGVLTA 332 Query: 302 V-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATL 360 V P G A+ R+T +DI++ G + K+FRIGHLG D +++ + +E L Sbjct: 333 VMMPEGHSADAFRATTLAHYDISLGNGLSKVADKVFRIGHLGDFNDLMLMATLSGVEMGL 392 Query: 361 IELG 364 + G Sbjct: 393 AKAG 396 Lambda K H 0.317 0.134 0.386 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: 412 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: 384 Length of database: 422 Length adjustment: 31 Effective length of query: 353 Effective length of database: 391 Effective search space: 138023 Effective search space used: 138023 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 (21.7 bits) S2: 50 (23.9 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