Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate PP_1872 PP_1872 glutamate-pyruvate aminotransferase
Query= curated2:P63499 (429 letters) >FitnessBrowser__Putida:PP_1872 Length = 403 Score = 570 bits (1469), Expect = e-167 Identities = 278/402 (69%), Positives = 334/402 (83%), Gaps = 1/402 (0%) Query: 28 FAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALP 87 F++S KL +V Y+IRGPV +HA RLE EGHRILKLNIGNPAPFGFEAPD I++D+I+ LP Sbjct: 3 FSKSNKLANVCYDIRGPVLKHAKRLEEEGHRILKLNIGNPAPFGFEAPDEILQDVIRNLP 62 Query: 88 YAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQV 147 AQGYSDS+G+ SAR+AV+ +Y ++D+YLGNGVSELI M++QALL+NGD+V Sbjct: 63 TAQGYSDSKGLFSARKAVM-QYCQQKDIEGVTIEDIYLGNGVSELIVMSMQALLNNGDEV 121 Query: 148 LIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTG 207 LIP+PDYPLWTA+ SLAGG PVHYLCDE W PD+ D+++KIT TKALV+INPNNPTG Sbjct: 122 LIPAPDYPLWTAAVSLAGGKPVHYLCDEQADWFPDLEDIKAKITPNTKALVIINPNNPTG 181 Query: 208 AVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAY 267 AVYS E+L M++LAR+H L++ +DEIYDKILYD+A HIS AS+APD+LCLTFNGLSK+Y Sbjct: 182 AVYSKELLLGMLELARQHNLVVFSDEIYDKILYDEAVHISTASLAPDLLCLTFNGLSKSY 241 Query: 268 RVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLP 327 RVAG+R+GWL I+GPK HA S+IEGI +LANMRLC NVPAQHAIQ ALGG+QSI DLVLP Sbjct: 242 RVAGFRSGWLIISGPKHHAHSYIEGIDMLANMRLCANVPAQHAIQTALGGYQSINDLVLP 301 Query: 328 GGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKIL 387 GRLLEQR+ + LN+IPGVSCVKP GALYAFPR+DP+V I +DE+ LDLLLSEK+L Sbjct: 302 PGRLLEQRNRTYELLNDIPGVSCVKPMGALYAFPRIDPKVCPILNDEKFALDLLLSEKLL 361 Query: 388 VTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 + QGT FNWP PDH R+VTLP DL AAI R+GNFL Y Q Sbjct: 362 IVQGTAFNWPWPDHFRVVTLPRVDDLEAAIGRIGNFLKGYSQ 403 Lambda K H 0.320 0.138 0.419 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: 621 Number of extensions: 16 Number of successful extensions: 2 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: 429 Length of database: 403 Length adjustment: 31 Effective length of query: 398 Effective length of database: 372 Effective search space: 148056 Effective search space used: 148056 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 (21.8 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