Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate 353246 BT3720 putative aspartate aminotransferase (NCBI ptt file)
Query= curated2:O58489 (391 letters) >FitnessBrowser__Btheta:353246 Length = 383 Score = 250 bits (639), Expect = 4e-71 Identities = 143/372 (38%), Positives = 218/372 (58%), Gaps = 14/372 (3%) Query: 21 IRELFERASKME----DVISLGIGEPDFDTPKNIKEAAKRALDEGWTHYTPNAGIPELRE 76 + ++ ERA++++ DVI L +GEPDFD P + EAAK A D THYT + G PELR Sbjct: 16 VMDVLERANELQKQGVDVIHLEVGEPDFDVPACVAEAAKAAYDRHLTHYTHSLGDPELRR 75 Query: 77 AVVEYYKKFYGIDIEVENVIITAGAYEGTYLAFESLLERGDEVIIPDPAFVSYAEDAKVA 136 + +Y++ YG+ ++ + +++T+G+ L L EVI+ +P + Y A Sbjct: 76 EIAAFYQREYGVTVDPDCIVVTSGSSPSILLVLMLLCNSDSEVILSNPGYACYRNFVLAA 135 Query: 137 EAKPVRIPLREENNFLPDPNELLEKISKNTRMIVINYPNNPTGATLDKELAKTIADIAED 196 +AKPV +PL EEN D + + ++ +T I IN P NPTG LD+ +++A + Sbjct: 136 QAKPVLVPLSEENGLQYDIEAIRKCVTPHTAGIFINSPMNPTGMLLDESFLRSVASL--- 192 Query: 197 YNIYILSDEPYEHFIYEDAKHYPMIKFAPENTILANSFSKTFAMTGWRLGFVVAPSQVIK 256 + I+SDE Y +YE H ++++ + +L N FSK FAMTG RLG+++AP ++ Sbjct: 193 -GVPIISDEIYHGLVYEGRAH-SILEYTDKAFVL-NGFSKRFAMTGLRLGYLIAPKSCMR 249 Query: 257 EMTKLHAYVIGNVASFVQIAGIEALRSEESWKAVEEMKKEYNERRKIVVKRLKNMPGIKV 316 + KL + +S Q AGI ALR +S VE MK+ Y+ERR+ ++ RL+ M G ++ Sbjct: 250 SLQKLQQNLFICASSIAQQAGIAALRQADS--DVERMKQIYDERRRYMISRLREM-GFEI 306 Query: 317 K-EPKGAFYVFPNISGTGMSSEKFSEWLLEKARVVVIPGTAFGRMGEGYVRISYATSKEK 375 K EP+GAFY+F + S +F+ +LE A V + PG FG GEGYVR SYA S E Sbjct: 307 KVEPQGAFYIFADARKFTTDSYRFAFDVLENAHVGITPGIDFGTGGEGYVRFSYANSLES 366 Query: 376 LIEAMNRIEKAL 387 + E ++RI + L Sbjct: 367 IREGLDRISQYL 378 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: 353 Number of extensions: 16 Number of successful extensions: 4 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: 383 Length adjustment: 30 Effective length of query: 361 Effective length of database: 353 Effective search space: 127433 Effective search space used: 127433 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 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