Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_011190179.1 DP_RS14870 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_000025945.1:WP_011190179.1 Length = 395 Score = 340 bits (871), Expect = 5e-98 Identities = 172/389 (44%), Positives = 247/389 (63%), Gaps = 5/389 (1%) Query: 6 LSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAEK 65 +S +++ K SWIRK+F++G ++K EFG + VFDFSLGNP PP F + L + A Sbjct: 3 ISSKMKIFAEKSSWIRKMFEQGGKMKAEFGAENVFDFSLGNPDAPPPAQFDQVLAKIAAD 62 Query: 66 ---GSHGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPGE 122 G+H Y+ N G L RE VA + A ++++ GA G +NV +KS++NPG+ Sbjct: 63 NGPGTHSYMPNGGHLWVREAVAGQMAKEQGVKVVASDMLLSCGAAGGINVIMKSLLNPGD 122 Query: 123 EVIILAPYFAEYKLYIENYGGKAVSCPLTSRFEIDIEAVRQSITPQTKGLILNTPHNPTG 182 EVI LAPYF EY Y++N+GGK+ F D+ A+R++I+ +TK +I+N+P+NPTG Sbjct: 123 EVIFLAPYFVEYDFYVDNHGGKSRVVQTDENFNPDMAAIREAISEKTKAIIINSPNNPTG 182 Query: 183 TVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYDE-ELANPFQSYHRVILASSF 241 + S++ + +LG LL E+ EK G TIY++ DEPY ++ YD E+ + F +Y I+ SS+ Sbjct: 183 QIYSKEILAELGLLLTEMGEKFGSTIYLISDEPYRKITYDGIEVPSIFAAYSNSIIVSSY 242 Query: 242 SKDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRVDA 301 SKDL + GER+GY+ + + + L++A NR LGFVNAP +MQR +A + + VD Sbjct: 243 SKDLSLPGERIGYVAVHPGISEKAELVSAMTLANRILGFVNAPALMQRVIAELQGISVDN 302 Query: 302 SAYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSSGF 361 Y RR+ IL EAGF+F PKG F++FPKSPIED+VAFC Q+ K+L VP GF Sbjct: 303 ERYARRREAFCQILTEAGFDFVPPKGAFYIFPKSPIEDDVAFCA-ILQEEKILAVPGRGF 361 Query: 362 GMSGHFRLSFSVPIEQIKNSRDIFISLYK 390 G G+ RL+F VP E I S F Y+ Sbjct: 362 GAPGYIRLAFCVPDETIAGSAAAFKRAYQ 390 Lambda K H 0.320 0.139 0.396 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: 425 Number of extensions: 17 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: 393 Length of database: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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 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