Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012281785.1 HM1_RS02935 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000019165.1:WP_012281785.1 Length = 397 Score = 231 bits (590), Expect = 2e-65 Identities = 137/396 (34%), Positives = 220/396 (55%), Gaps = 13/396 (3%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M L+K + S+ A+AKK+ ++G +I G G+PDF TP HV AA A++ G Sbjct: 1 MNLSKKGLSIHPSPTLSIDAKAKKMRSEGVDVIGFGAGEPDFDTPDHVKQAAIAAIEAGF 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y ++G LE +QA+ K+K D P +++ G K ++ A + PG E+I P Sbjct: 61 TKYTPASGTLELKQAICDKLKAENGVDYAPANIIVSNGAKHSLVNAFEAICNPGDEVIIP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y M+ + PV TE+ KF E+I +T KT+ L+L +P+NPTG Sbjct: 121 APYWVSYPEMVKLVDAVPVFVYTTEESRFKFTVEQIKQALTSKTKALVLNSPSNPTGMVY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPD-LQDRLIVLDGWSKAY 239 K + +A+ L + ++SDEIY + IYD E + + D ++++ I+++G SKAY Sbjct: 181 SKEELAEIAD-LAVEYGIFVISDEIYEKLIYDDFEHVSIASINDKIKEQTIIVNGVSKAY 239 Query: 240 AMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQR 299 +MTGWR+G++ + + + ++ S N+ +Q A +AA+ GP D + M+ +F +R Sbjct: 240 SMTGWRIGYTASNAPIAKIMANIQSHATSNPNSIAQKAALAAITGPQDIVGTMVGEFVRR 299 Query: 300 RKLIHEGLNSLPGVECSLPGGAFYA---FPKVIGT-----GMNGS-EFAKKCMHEAGVAI 350 R + E +N++PG+ C P GAFY K+IG+ +NGS +FA + +A VA+ Sbjct: 300 RDYMVERINAIPGLSCLKPNGAFYVMMNISKIIGSTFAGRRINGSDDFADLLLEQAQVAL 359 Query: 351 VPGTAFGKTCQDYVRFSYAASQDNISNALENIKKML 386 VPG+ FG +VR SYA S +NI+ L I+ L Sbjct: 360 VPGSGFG--IDTHVRLSYATSMENITEGLNRIENFL 393 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: 417 Number of extensions: 20 Number of successful extensions: 5 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: 397 Length adjustment: 31 Effective length of query: 356 Effective length of database: 366 Effective search space: 130296 Effective search space used: 130296 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