Align Alanine--glyoxylate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_005815362.1 DHAF_RS24160 alanine--glyoxylate aminotransferase family protein
Query= SwissProt::P43567 (385 letters) >NCBI__GCF_000021925.1:WP_005815362.1 Length = 390 Score = 171 bits (433), Expect = 3e-47 Identities = 116/363 (31%), Positives = 189/363 (52%), Gaps = 30/363 (8%) Query: 6 DTLLIPGPIILSGAVQKALDVPSLGHTSPEFVSIFQRVLKNTRAVFKSAAASKSQPFVLA 65 + LLIPGP + + +AL + HT P V F+ L T+ +F + + FV+A Sbjct: 5 EMLLIPGPTPVVDEIYEALAQETYSHTDPRLVKRFKNSLDMTKRLFNT----DGEVFVVA 60 Query: 66 GSGTLGWDIFASNFILSKAPNKNVLVVSTGTFSDRFADCLRSYGAQVDVVRPLKIGESVP 125 GSGTL ++ N + AP + +LV+S G F DRF +++G QV+V++ + G+ V Sbjct: 61 GSGTLSMEMAIVNTV---APGEKILVISHGYFGDRFIPLAQAHGIQVEVLQS-QWGKHVE 116 Query: 126 LELITEKLSQNSYGAVTVTHVDTSTAVLSDLKAISQAIKQTSPETFFVVDAVCSIGC--- 182 + + EKL++ + AVTVTH DTST V+S+L+ + A+K+ P F++D VC+ Sbjct: 117 ISAVEEKLAEGGFKAVTVTHADTSTGVMSNLEELVPAVKKYGP--LFILDGVCASAAIEE 174 Query: 183 ---EEFEFDEWGVDFALTASQKAIGAPAGLSISLCSSRFMDYALNDSKNGHVHGYFSSLR 239 +E+ ++ +D LT SQKAIG P GL+I + + K V Y+ + Sbjct: 175 NMQKEYGHPDYRIDLVLTGSQKAIGVPPGLAIVAFGPKALKAREAMDK---VAAYYMDIL 231 Query: 240 RWTPIMENYEAGKGAYFATPPVQLINSLDVALKEILEEGLHKRWDLHREMSDWFKDSLVN 299 RW P M++ G Y+AT PV +I + + ++ ++ EGL R+ H + + L Sbjct: 232 RWLPTMQD----PGKYYATHPVNMIYAYEKGMELVMAEGLEARYKRHAALGKAVRAGLA- 286 Query: 300 GLQLTSVSRYPSNMSAHGLTAVYVADPPDVIAF---LKSHGVVIAGGIHKDIGPKYIRIG 356 Q + P ++A L+ + + + F L G+VIAG + ++ K RIG Sbjct: 287 --QYGMRALAPEEIAAPTLSCILYPEGVNDAEFRSKLAEKGMVIAGSL-ANLAGKAFRIG 343 Query: 357 HMG 359 HMG Sbjct: 344 HMG 346 Lambda K H 0.319 0.134 0.397 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: 356 Number of extensions: 19 Number of successful extensions: 7 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: 385 Length of database: 390 Length adjustment: 30 Effective length of query: 355 Effective length of database: 360 Effective search space: 127800 Effective search space used: 127800 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 (21.8 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