Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_027721528.1 H589_RS0107920 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000425265.1:WP_027721528.1 Length = 386 Score = 202 bits (514), Expect = 1e-56 Identities = 124/376 (32%), Positives = 205/376 (54%), Gaps = 18/376 (4%) Query: 18 VLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVT 77 VL +A+++E +G+ +IH+ +G+PDF TP + A +A+D+G Y S GI E R+A++ Sbjct: 19 VLEKAQQMEREGRSIIHMEIGEPDFDTPDCIKKACCEAMDKGETHYTHSLGIPELREAIS 78 Query: 78 RKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGST 137 + K YN D+DP+RV+I G P M + G +I P + Y + I++ G+ Sbjct: 79 KYHKDRYNVDVDPDRVIITQGTSPAMLLLFTFILDKGDNVIVSDPCYACYSNFISFAGAE 138 Query: 138 PVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKHPH 197 E+ ++ PE I I KT+ +++ +P+NPTG+ + + +A G+ Sbjct: 139 ANRITTFEEDGFQYRPEAIKKAINTKTKAILINSPSNPTGTLLSPERMKEIA-GMGPW-- 195 Query: 198 VAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVWPEELIP 257 I+SDEIY +Y KE + + D VL+G+SK +AMTGWR+G+ + PE+ + Sbjct: 196 --IISDEIYHGLVYGEKE----HSILEYTDHAFVLNGFSKLFAMTGWRLGYIISPEKYVR 249 Query: 258 HVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGVECSL 317 + KL N N+ +Q AG+AAL D ++ + +D+RRK + + L + G + + Sbjct: 250 PLQKLCQNFFISANSMAQRAGVAALTESWDDVNRIKNTYDERRKYMLKRLREM-GFDIKV 308 Query: 318 -PGGAFYAF--PKVIGTGMNGS--EFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQ 372 P GAFY K + +GS + A + +AG+ + PG FG + Y+R SYA S Sbjct: 309 EPTGAFYVLVNMKHLAAKFDGSSLKLAFDILEQAGIGVTPGIDFGDGAEGYIRLSYANSI 368 Query: 373 DNIS---NALENIKKM 385 +N++ + LEN KM Sbjct: 369 ENLAEGMDRLENYVKM 384 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: 395 Number of extensions: 10 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: 387 Length of database: 386 Length adjustment: 30 Effective length of query: 357 Effective length of database: 356 Effective search space: 127092 Effective search space used: 127092 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