Align Aspartate aminotransferase; AAT; AspAT; EC 2.6.1.1 (characterized)
to candidate 3607759 Dshi_1168 aminotransferase class I and II (RefSeq)
Query= SwissProt::Q82DR2 (408 letters) >FitnessBrowser__Dino:3607759 Length = 391 Score = 174 bits (441), Expect = 4e-48 Identities = 123/380 (32%), Positives = 185/380 (48%), Gaps = 22/380 (5%) Query: 31 AKALKAAGRPVIGFGAGEPDFPTPDYIVQAAIEACSNPKYHRYTPAGGLPELKAAIAAKT 90 A+ +AAGR +I G+P P + A+ A + YT A GLPEL+ AIA Sbjct: 21 ARRAEAAGRHIIHMEVGQPGTAAP-LPARRAVAAQLDQDAMGYTVALGLPELRRAIAGLY 79 Query: 91 LRDSGYEVDASQVLVTNGGKQAIYEAFAAILDPGDEVIVPAPYWTTYPESIRLAGGVPVD 150 R G ++D ++V+VT+G A AF D G V V P + +Y + ++ PV Sbjct: 80 ARWYGVDLDPARVVVTSGSSAAFLLAFTTYFDAGARVGVAEPGYPSYRQILKALSLAPVG 139 Query: 151 VVADETTGYRVSVEQLEAARTENTKVLLFVSPSNPTGAVYTREQIEEIGRWAAEKGLWVL 210 + TG+R++ E L A + SP+NPTG + R+ + + ++ + Sbjct: 140 LPTQPETGHRMTAEALAQADIAGA---IIASPNNPTGTMLDRDGLGALIAACRDRDRVFI 196 Query: 211 TDEIYEHLVYGDAEFHSLPVVVPELADKCIVVNGVAKTYAMTGWRVGWVIGPKDVIKAAT 270 +DEIY L YGD +L E++D V+N +K ++MTGWR+GW++ P+ ++ Sbjct: 197 SDEIYHGLHYGDRAVSAL-----EISDDVCVINSFSKYFSMTGWRIGWLVVPEAQVRVVE 251 Query: 271 NLQSHATSNVSNVAQVAALAAVSGDLTAVAEM-REAFDRRRKTIVRMLNEIGGVLCPEPE 329 L + +VAQ+AAL A+ E R + R+ ++ L G P+ Sbjct: 252 RLAQNMFICAPHVAQIAALGALGDAARPELEANRAVYAANRQLVIDGLRAAGLDAFAPPD 311 Query: 330 GAFYAYPSVKALLGKEIRGKRPQDTVELAALILEEAEVAVVPGEAFGT---PGYLRLSYA 386 GAFY Y AL D+ LAA ILE+A VAV PG F G LRLSYA Sbjct: 312 GAFYVYVDTGAL---------SSDSRTLAADILEKAGVAVTPGLDFDPVRGHGTLRLSYA 362 Query: 387 LGDEDLVEGVSRIQKLLSEA 406 ED+ EG++R+ + A Sbjct: 363 RATEDIAEGMTRLTNYFAAA 382 Lambda K H 0.315 0.132 0.381 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: 360 Number of extensions: 13 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: 408 Length of database: 391 Length adjustment: 31 Effective length of query: 377 Effective length of database: 360 Effective search space: 135720 Effective search space used: 135720 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: 42 (22.0 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