Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_084657311.1 N745_RS0105535 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000526715.1:WP_084657311.1 Length = 399 Score = 353 bits (906), Expect = e-102 Identities = 181/395 (45%), Positives = 253/395 (64%), Gaps = 6/395 (1%) Query: 10 DRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGY 69 +RI++LPPYVF ELKA+AR +G D+ID GMGNPD TP+ +VD I+ +Q H Y Sbjct: 8 ERIKRLPPYVFNITGELKAEARRRGEDIIDFGMGNPDQDTPKHIVDKLIEVVQREGTHRY 67 Query: 70 PPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSP 129 +G RRAI NWY ++ V LD ++EA+ +GSKEGL+HLA+A V GD VLVP+P Sbjct: 68 SVSQGIPRLRRAICNWYKTKFDVDLDYETEAVVTIGSKEGLAHLALATVEKGDTVLVPNP 127 Query: 130 AYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPR 189 AYP H G VIAG + + + P+ D+ +L +E K K+L N+P NPT T Sbjct: 128 AYPIHPYGFVIAGADIRHVRMTPDVDFFDELEKAIKESWPKPKMLVLNFPGNPTTQTVDL 187 Query: 190 EFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAG 249 FFE++VA A+++ I ++HDL YA++AFDGY+ S++++ GAKDI VEF+TLSK+YNM G Sbjct: 188 HFFEKVVAIAKEHNIWVIHDLAYADIAFDGYKAPSIMQVEGAKDIAVEFYTLSKSYNMPG 247 Query: 250 WRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFL 309 WRVGF+VGN ++Q L+ +K+ LDYG F +Q AA AL+ P + E+ Y++RRD L Sbjct: 248 WRVGFMVGNPVLVQALKRMKSYLDYGTFTPIQVAAIAALEGPQDCVQEISDMYKSRRDVL 307 Query: 310 IQGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEG 366 QGL +GW V KATM++W P MGS +F+ LL V V PG FG G+ Sbjct: 308 CQGLNSIGWKVEPPKATMFVWAPIPEEYRDMGSLEFSKKLLTDAKVAVAPGIGFGDYGDD 367 Query: 367 YVRISLIADCDRLGEALDRIKQAGIRYRPEALVSA 401 +VR LI + R +A+ I+ +R + L+ + Sbjct: 368 HVRFGLIENEHRTRQAIRGIRD---MFRKDGLIKS 399 Lambda K H 0.321 0.140 0.427 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: 492 Number of extensions: 21 Number of successful extensions: 2 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: 403 Length of database: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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