Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013135865.1 ARNIT_RS10285 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000092245.1:WP_013135865.1 Length = 390 Score = 233 bits (594), Expect = 7e-66 Identities = 133/389 (34%), Positives = 214/389 (55%), Gaps = 6/389 (1%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 MK+AK ++ L ++ A ++L+AQGK ++ G+PDF TP V AA KA+ +GH Sbjct: 1 MKIAKRMENLSPSVTMAITALGRELKAQGKDILSFSAGEPDFDTPDIVKQAAIKAIQDGH 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y GI E ++A+ K+KK + + + + ++I G K +++ Q E G E+I P Sbjct: 61 TKYTAVEGITETKKAIITKLKKDHGLNYNLDEIIISNGAKHSLFNLFQVLIEEGDEVIIP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y + ++ PV + + K E+I + IT KT++L+L P+NPTG+ Sbjct: 121 APYWVTYPEQVKFSDGVPVFIETDDTTGFKVTAEQIKAAITPKTKVLLLNTPSNPTGAIY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAY 239 K + + + L + + + SDE+Y + IYDGK+ T D+ R + ++G SKA Sbjct: 181 TKEELTAIGKVL-EGTDILVFSDEMYEKIIYDGKKFCTAAEVSDDMFQRTVTINGLSKAV 239 Query: 240 AMTGWRMGWSVWPEE-LIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVK-FD 297 AMTGWR G+ P++ L+ + KL S VN+ +Q+A I AL+G DA E+M K F+ Sbjct: 240 AMTGWRFGYLATPQKNLVKAMTKLQGQVTSNVNSITQYAAIPALEGEADATIEIMRKEFE 299 Query: 298 QRRKLIHEGLNSLPGVECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFG 357 +RR + E N++ G+ C P GAFY F + + +F + GVA+VPG AFG Sbjct: 300 KRRDISVEKFNAIKGISCLKPDGAFYLFVNIKELTFDSMKFCSDLLELKGVAVVPGLAFG 359 Query: 358 KTCQDYVRFSYAASQDNISNALENIKKML 386 + Y RFS+A D+I + I++ + Sbjct: 360 --TEGYFRFSFATDLDSILKGIARIEEFV 386 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: 396 Number of extensions: 31 Number of successful extensions: 6 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: 390 Length adjustment: 30 Effective length of query: 357 Effective length of database: 360 Effective search space: 128520 Effective search space used: 128520 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 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