Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013722554.1 ALIDE2_RS15675 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000204645.1:WP_013722554.1 Length = 405 Score = 221 bits (563), Expect = 3e-62 Identities = 136/392 (34%), Positives = 198/392 (50%), Gaps = 13/392 (3%) Query: 3 LAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHG 62 L + L + + + V+ + G +I L G+PDF TP HV +A A+ GH Sbjct: 8 LNRFLAQAKPSATYKVMDRVAARRSAGAQVISLCAGEPDFDTPGHVREAGIAAIRAGHTR 67 Query: 63 YVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTP 122 Y G+ R+A+ K ++ ++D L+ GGK ++ A+ G E+I P P Sbjct: 68 YTQVAGLRALREAIAAKFQRENGLELDWRGTLVCSGGKQAIFNALAATLNEGDEVIMPAP 127 Query: 123 AFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEK 182 + Y ++ GS + K P + + IT +TR LIL +P+NPTG+ + Sbjct: 128 YWVSYPEIVQLCGSKAITVACNAGNGFKLTPAALQAAITPRTRWLILNSPSNPTGAVYSR 187 Query: 183 SAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAYAM 241 + + LAE L HPHV +LSD+IY I+DG T P L++R++ ++G SKAYAM Sbjct: 188 AELQALAEVLLAHPHVLVLSDDIYEHLIFDGLAFFTIAQVEPRLRERVLTMNGVSKAYAM 247 Query: 242 TGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRK 301 TGWR+G+ P LI + KL S SQ A +AAL GP D I + F +RR Sbjct: 248 TGWRIGFCTGPGWLIEAMEKLQGQQTSGACTISQHAALAALTGPQDFIQQSRTAFQRRRD 307 Query: 302 LIHEGLNSLPGVECSLPGGAFYAFPKVIG----TGMNGSEF------AKKCMHEAGVAIV 351 ++ E LN PG+ C +P GAFYAF G T G++ A + EAGVA V Sbjct: 308 MVVESLNQAPGLHCEVPQGAFYAFASCEGLIGKTTPGGTQLDTDEAVATALLGEAGVAAV 367 Query: 352 PGTAFGKTCQDYVRFSYAASQDNISNALENIK 383 G+AFG Y+R +YA + A E I+ Sbjct: 368 HGSAFG--LGPYLRVAYAIDDAALRGACEAIR 397 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: 18 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: 405 Length adjustment: 31 Effective length of query: 356 Effective length of database: 374 Effective search space: 133144 Effective search space used: 133144 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