Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_205630628.1 AU252_RS03265 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O58489 (391 letters) >NCBI__GCF_001484605.1:WP_205630628.1 Length = 387 Score = 210 bits (535), Expect = 5e-59 Identities = 125/375 (33%), Positives = 202/375 (53%), Gaps = 12/375 (3%) Query: 19 SKIRELFERASKMEDVISLGIGEPDFDTPKNIKEAAKRALDEGWTHYTPNAGIPELREAV 78 ++IRE+ E A I L IGEP F P++I EA LD T+YTPNAGIP LREA Sbjct: 14 NQIREITEAAWHTPGAIVLSIGEPGFALPRHILEAGMACLDRDETNYTPNAGIPALREAF 73 Query: 79 VEYYKKFYGIDIEV--ENVIITAGAYEGTYLAFESLLERGDEVIIPDPAFVSYAEDAKVA 136 +++ G++ + E V + GA +G + A LL GDE++IP+P + ++A +++ Sbjct: 74 ATRFRERAGLNTSLGAERVYVVDGAQQGLHFAMSLLLSPGDEILIPNPGYPTFAMTSRLL 133 Query: 137 EAKPVRIPLREENNFLPDPNELLEKISKNTRMIVINYPNNPTGATLDKELAKTIADIAED 196 A PV PL E++F P ++ I+ TR++++N P+NP GA L +L + + D+A Sbjct: 134 NAVPVGYPLYPEHDFQPRIQDIEALITDRTRVLILNSPSNPLGAVLGADLTRQLVDLARK 193 Query: 197 YNIYILSDEPYEHFIYEDAKHYPMIKFAPE-----NTILANSFSKTFAMTGWRLGFVVAP 251 +++I+SDE YE F Y D H +F + + + SKT+ +TG R+G +V P Sbjct: 194 RDLWIISDECYEAFTY-DVPHVSPARFDSDVPGEARVFTSLTLSKTYGLTGLRIGALVCP 252 Query: 252 SQVIKEMTKLHAYVIGNVASFVQIAGIEALRSEESWKAVEEMKKEYNERRKIVVKRLKNM 311 + ++M + ++ VAS Q A + AL + + V + Y R + Sbjct: 253 PGLEQKMNNVMEAIVSCVASPSQYAALAALTGPQDY--VRHAHEHYRANRD-AASAVLEA 309 Query: 312 PGIKVKEPKGAFYVFPNISGTGMSS-EKFSEWLLEKARVVVIPGTAFGRMGEGYVRISYA 370 GI +GAFY++ N+S ++ L + V + PGTAFG +GEG+VRI+ Sbjct: 310 KGIPYLSAQGAFYLWANVSHVSDGDVRSWARRFLADSGVALAPGTAFGSIGEGWVRIALC 369 Query: 371 TSKEKLIEAMNRIEK 385 ++ L+E + R+ K Sbjct: 370 GTRNDLVEGVGRLPK 384 Lambda K H 0.316 0.135 0.382 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: 362 Number of extensions: 16 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: 391 Length of database: 387 Length adjustment: 30 Effective length of query: 361 Effective length of database: 357 Effective search space: 128877 Effective search space used: 128877 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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