Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate WP_080517386.1 RSPH17029_RS20165 aspartate aminotransferase family protein
Query= SwissProt::Q84P54 (515 letters) >NCBI__GCF_000015985.1:WP_080517386.1 Length = 461 Score = 432 bits (1110), Expect = e-125 Identities = 210/435 (48%), Positives = 293/435 (67%), Gaps = 1/435 (0%) Query: 70 LAPFTAGWQSTDVDPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQ 129 L P+T PLII + +G HVYD +GR+YI+ LAGLW A+G +EPRL +AA +Q Sbjct: 18 LHPYTNARAHERNGPLIITRGQGVHVYDSEGREYIEGLAGLWSVAVGFSEPRLAEAAARQ 77 Query: 130 LNTLPFYHSFWNRTTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNA 189 + LP+YH+F + +P + LA++L++M T + + FFTNSGSEANDT VKLVW+ NNA Sbjct: 78 MAELPYYHTFAGKAHEPQIRLAEKLVEM-TPVALTRVFFTNSGSEANDTVVKLVWFMNNA 136 Query: 190 LGRPNKKKFIARAKAYHGSTLISASLTGLPALHQNFDLPAPFVLHTDCPHYWRYHLPGET 249 LGRP KKKF++R K YHG T+ S SLTGLP H+ FDLPA V+H CPH+WR+ GE+ Sbjct: 137 LGRPQKKKFLSRIKGYHGITIASGSLTGLPVNHKGFDLPAIPVVHLGCPHHWRFGAEGES 196 Query: 250 EEEFSTRLAKNLEDLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILF 309 E +F RL + E+ IL EGPET+AAFI EPVMGAGGVI PP Y+ I+A+ +KYDIL Sbjct: 197 EADFCARLLREAEETILAEGPETVAAFIGEPVMGAGGVIVPPDGYWSGIEALCRKYDILL 256 Query: 310 IADEVICAFGRLGTMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNK 369 ++DEVI FGR G +G + + PD++ +K L+S+YMP+ AVL++ +V +I + Sbjct: 257 VSDEVINGFGRTGARWGCEKFGFTPDILVTSKQLTSSYMPLAAVLMTDKVYQIIADHTET 316 Query: 370 LGSFSHGFTYSGHPVACAVALEAIKIYKERNMVERVNRISPKFQEGLKAFSDSPIIGEIR 429 +G+ HGFT SGHPVA AV LE + + +ER+++ R+ FQ+GL+AF D+P++GE+R Sbjct: 317 VGTLGHGFTGSGHPVATAVGLENLTVIEERDLMGNAARLERPFQDGLRAFRDNPLVGEVR 376 Query: 430 GLGLILATEFANNKSPNDHFPPEWGVGAYFGAQCQKNGMLVRVAGDTIMMSPPFVVTPEE 489 G GLI A E +++ F P VGA A + G+L R GDT+ + PP +VT + Sbjct: 377 GTGLIAAIEMVADRATKRSFEPLGKVGARAAAFAAEEGLLCRALGDTLALCPPLIVTEAD 436 Query: 490 LDELIRIYGKALRET 504 + ++ G+AL T Sbjct: 437 VGGILERMGRALDRT 451 Lambda K H 0.318 0.135 0.402 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: 569 Number of extensions: 19 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: 515 Length of database: 461 Length adjustment: 34 Effective length of query: 481 Effective length of database: 427 Effective search space: 205387 Effective search space used: 205387 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. 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