Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 8500823 DvMF_1564 aminotransferase class I and II (RefSeq)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Miya:8500823 Length = 400 Score = 196 bits (498), Expect = 1e-54 Identities = 138/409 (33%), Positives = 207/409 (50%), Gaps = 32/409 (7%) Query: 6 TVKEAGFQPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASD 65 T E+ + A R+ +I +S + AA + + LG G P F TP+H+ +A Sbjct: 5 TSSESPLRVAERVRNIRISATKLMPMLAAKVGG----CVSLGQGVPSFRTPDHIVEAVCR 60 Query: 66 AIHRGET--KYTALDGTPELKKAIREKFQRENGLAYELD-EITVATGAKQILFNAMMASL 122 A+ T +Y+ G P L++AI G ++ + EI V GA + L M+ + Sbjct: 61 ALRDDPTAGRYSLQPGMPALREAIAADILARKGARFDPETEIGVTVGAMEALVMIMLTVV 120 Query: 123 DPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNS 182 + GDEVIIP+P + S+++ V + EG PV + A+ + L E + A+TPRTR +++ S Sbjct: 121 ERGDEVIIPSPGYASHAEQVLMAEGVPVHVPLRAAD-WGLDVEAVRFAVTPRTRAIIVCS 179 Query: 183 PSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIVYD---GFRFVTPAQLEPGLKN 239 P NP+G Y AD R L ++ L V L+VDD Y+++VY G +P +P L+ Sbjct: 180 PGNPTGGVYDDADVRALCDLALERDLV-LIVDDTYDYMVYGEQPGTPRFSPVS-QPELRR 237 Query: 240 RTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQD 299 +TVN SK YA+TGWR+GY + + V C ++SQ A++AAL GPQD Sbjct: 238 HVITVNSFSKKYALTGWRVGYVAADAAWMAELLKVHDATAVCAPTVSQHAALAALTGPQD 297 Query: 300 FLKERTESFQRRRDLVVNGLNAIDGLDCRV-PEGAFYTFSGCAGVLGKVTPSGKRIKTDT 358 + + RRDL L+A+ V P GAFY + + TD Sbjct: 298 CVDVMRAALTARRDLTCRRLDALAPHFAYVPPRGAFYAMA-------------RYTFTDA 344 Query: 359 D---FCAYLLEDAHVAVVPGSAFGLS--PFFRISYATSEAELKEALERI 402 D +LE+A V VPG +FG + R+S+ EAEL EA +RI Sbjct: 345 DSMTVARRMLEEARVITVPGGSFGPTGERHLRLSFGMDEAELTEAFDRI 393 Lambda K H 0.318 0.134 0.393 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: 440 Number of extensions: 28 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: 410 Length of database: 400 Length adjustment: 31 Effective length of query: 379 Effective length of database: 369 Effective search space: 139851 Effective search space used: 139851 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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