Align Gamma aminobutyrate transaminase 2; Gamma-aminobutyrate transaminase isozyme 2; LeGABA-TP2; SlGABA-T2; EC 2.6.1.96 (characterized)
to candidate WP_022947828.1 H035_RS0104615 aspartate aminotransferase family protein
Query= SwissProt::Q84P53 (458 letters) >NCBI__GCF_000421465.1:WP_022947828.1 Length = 463 Score = 135 bits (339), Expect = 4e-36 Identities = 118/430 (27%), Positives = 197/430 (45%), Gaps = 52/430 (12%) Query: 32 AEGSYVYGVNGKKYLDSLSGLWCTVLGGSEPRLIEAASKQLNKSAFYHSFWNRTTKPSLD 91 A G Y+Y +YLD LSG LG + P + A + L+ + + L Sbjct: 44 ARGPYLYDQEDNEYLDLLSGFGVFALGRNHPTIQSALREVLDLDLPDLVQMDVSILSGL- 102 Query: 92 LAKELINMFTANKMGKVFFTSSGSEANDTQVKLVWYYNNAIGRPNKKKIISRKNAYHGST 151 LA++L+ + T + K+FF +SG+EA + +K Y + +I+ ++A+HG T Sbjct: 103 LAEKLVQV-TPEPLTKLFFCNSGAEAVEAAIKFARYTTG------RSRILYCEHAFHGLT 155 Query: 152 YMTAGLSGLPSLHLKFDLPPPYILHTDCPHYWNYHLPGETEEEYSTRLANNLENL--ILK 209 L+G F P + D + N+LE L LK Sbjct: 156 LGALSLNGEEVFRQGFG---PLLPDCDAIPF------------------NDLEALERALK 194 Query: 210 EGPETVAAFIAEPVMGGAGVIIPPATYFEKIQAVLKKYDILFIADEVICGFGRLGTMFGC 269 E P AAFI EP+ G GV +P Y + + +KY LFIADE+ G GR G ++ Sbjct: 195 EQP--TAAFIVEPIQG-KGVNLPDDDYLTEAARLCRKYGALFIADEIQAGLGRTGRLWAI 251 Query: 270 DKYNIKPDLVSIAKALSGGYIPIGAVLVSEEISKVIMSQSNQLGVFCHGFTYSGHPVACA 329 + + ++PD++ +AKALSGG++P+GAV ++ + + ++ ++ V HG T+S + A A Sbjct: 252 EHWGVEPDMLLMAKALSGGFVPVGAVAMTAHVMDKVFNRMDRAVV--HGSTFSKNNPAMA 309 Query: 330 VALEALKIYKEKNITEVVNKLSPKLQEGLKAFIDS-PIIGEIRGTGLVLSTEFVDNKSPN 388 L L + +E+ + + L GL A D +RG GL+L+ EF K + Sbjct: 310 AGLATLSVIEEEKLLANAARQGEALIGGLNALTDKYEFFQAVRGKGLMLALEF--GKPRS 367 Query: 389 DPFPPEWGV----GTYFGSQC------QKHGMLVSFSGDHVNMA---PPFTLSLEELDEM 435 W + SQ ++H +L +G +N+ PP + ++++ + Sbjct: 368 LKLKTAWSLLETANKGLFSQMVTIPLFKRHRILSQVAGHGMNVVKFLPPLVIGAKDVEWI 427 Query: 436 ISIYGKALKD 445 +S L D Sbjct: 428 VSAMDDVLAD 437 Lambda K H 0.318 0.136 0.410 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: 492 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 458 Length of database: 463 Length adjustment: 33 Effective length of query: 425 Effective length of database: 430 Effective search space: 182750 Effective search space used: 182750 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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