Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__WCS417:GFF3717 Length = 401 Score = 214 bits (544), Expect = 4e-60 Identities = 129/389 (33%), Positives = 208/389 (53%), Gaps = 19/389 (4%) Query: 10 LGTESAFSVLAEA--KKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSN 67 LG + S+ A A +L AQG+ +++ +G+PDF TP H++ AA +A+ G Y + Sbjct: 10 LGIAPSPSIAANALVTELRAQGRDIVNFTVGEPDFDTPAHILAAASQAMHNGDTHYTSTT 69 Query: 68 GILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIY 127 G L RQA+ K+++ + + V+ GGK +Y+A+ G E+I TP + Y Sbjct: 70 GTLALRQAICLKLQQDNDLAYGLDEVVAGCGGKHVIYHALAATLNRGDEVIVHTPYWVSY 129 Query: 128 ESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDV 187 + +TPV E K P+ + IT +T+ +IL +PNNP+G+ ++ + Sbjct: 130 PDIARLNDATPVIIPGDESLGFKLSPDALEQAITARTKWVILNSPNNPSGAVYNETELLA 189 Query: 188 LAEGLKKHPHVAILSDEIYSRQIYD-GKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRM 246 LA+ L++HPHV I++DEIY IY + +P PDL+ R ++++G SK YAMTGWR+ Sbjct: 190 LAQVLRRHPHVLIMADEIYEHFIYGRARHVPLTRLAPDLKPRTLIVNGASKGYAMTGWRL 249 Query: 247 GWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEG 306 G+ P LI + KL+ + +C ++ SQ A +AA G I M ++ QRR + Sbjct: 250 GFGAGPAWLIAAIAKLLSQTTTCPSSLSQAAAVAAFTGDQAPIAAMREEYQQRRARMLAL 309 Query: 307 LNSLPGVECSLPGGAFYAFPKVIGTGMNG------------SEFAKKCMHEAGVAIVPGT 354 L +PG+ C+ P GAFY F V +G+ G ++ + + G+A V G Sbjct: 310 LADIPGLSCTPPDGAFYVFANV--SGLMGKLTPQGDRLDSDTQLVDYLLRDYGLATVSGA 367 Query: 355 AFGKTCQDYVRFSYAASQDNISNALENIK 383 A+G + YVR S+A+S + I +K Sbjct: 368 AYGMS--PYVRLSFASSSEVIEEGCRRLK 394 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: 366 Number of extensions: 14 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: 401 Length adjustment: 31 Effective length of query: 356 Effective length of database: 370 Effective search space: 131720 Effective search space used: 131720 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 09 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