Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF835 HP15_814 aspartate aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__Marino:GFF835 Length = 416 Score = 216 bits (551), Expect = 7e-61 Identities = 114/358 (31%), Positives = 193/358 (53%), Gaps = 2/358 (0%) Query: 25 LEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVTRKIKKLY 84 + A K +IHL +GQPD TP+HV+DA AL+ G GY + G+ E A+ K Y Sbjct: 52 MAATMKDVIHLSIGQPDLPTPKHVIDAYIDALNAGQTGYTMDAGLPELLVALRDYYGKRY 111 Query: 85 NKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGSTPVPYDLT 144 N+ + + +LI G MY AI PG + I P+F +Y +I G Sbjct: 112 NRKLTRDNILITSGATEAMYLAISATSAPGRQFIVTDPSFLLYAPLIRMNGGEVKFVQTR 171 Query: 145 EDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKHPHVAILSDE 204 + + + DP++++ + +T LIL NPNNPTG+ +S ++ + E + + + +DE Sbjct: 172 AENNHQLDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVETILEEC-AYRGIQVYADE 230 Query: 205 IYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVWPEELIPHVNKLII 264 +Y I+D ++ + N D ++ + +SK Y+M G R+GW + + I + + + Sbjct: 231 VYDHLIFDDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVGWVIASQAAIKSLRRFHM 290 Query: 265 NSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGVECSLPGGAFYA 324 + S N PSQFAG+AAL G + +M+ + +RR + E ++ P + PGGAF+A Sbjct: 291 FTTSVANTPSQFAGVAALTGDQQCVRDMVDIYRERRDKVVELVDQTPYMTGYKPGGAFFA 350 Query: 325 FPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQDNISNALENI 382 FP + ++GS+ A + + E GV +VPG AFG+ C + VR S++ + + + A + + Sbjct: 351 FPD-LPPHVDGSDLALRMLKETGVCMVPGDAFGEGCTNAVRISFSTTCEKLEEAFDRV 407 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: 444 Number of extensions: 17 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: 416 Length adjustment: 31 Effective length of query: 356 Effective length of database: 385 Effective search space: 137060 Effective search space used: 137060 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