Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 194 bits (492), Expect = 5e-54 Identities = 111/369 (30%), Positives = 190/369 (51%), Gaps = 3/369 (0%) Query: 14 SAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECR 73 +A+ + A + +G+ +I L +G PDF TP V DAA AL G Y G E R Sbjct: 16 AAWDIHFAAWTAKGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELR 75 Query: 74 QAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINY 133 A+ R + + ++PE V++ G + ++ A C E G E++ P P + YE+ + Sbjct: 76 AALARDVARRTGLPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRA 135 Query: 134 TGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLK 193 +G+T VP + L+ DP + + +T +TR + L P NPTG + ++ +A+ + Sbjct: 136 SGATLVPV-APDAATLRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLAR 194 Query: 194 KHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVWPE 253 +H + +++DE+Y+ +D + P + +R + ++ SK++AMTGWR GW V P Sbjct: 195 RHD-LWVVADEVYASLTFDRPHIG-IATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPA 252 Query: 254 ELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGV 313 L+ H+ L + + + Q A + A++ D+A+ M + +RR + E L S+PG+ Sbjct: 253 PLVAHMGTLALCMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGL 312 Query: 314 ECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQD 373 C P + V GTG+ EFA + E GV+++ AFG VR S+A S+ Sbjct: 313 RCLKPEAGMFMLVDVRGTGLPTMEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEA 372 Query: 374 NISNALENI 382 ++ A I Sbjct: 373 ELAEACRRI 381 Lambda K H 0.319 0.137 0.414 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: 387 Number of extensions: 26 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: 387 Length of database: 392 Length adjustment: 30 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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 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