Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate RR42_RS27405 RR42_RS27405 aminotransferase
Query= SwissProt::Q84P54 (515 letters) >FitnessBrowser__Cup4G11:RR42_RS27405 Length = 448 Score = 453 bits (1165), Expect = e-132 Identities = 218/432 (50%), Positives = 307/432 (71%), Gaps = 1/432 (0%) Query: 70 LAPFTAGWQSTDVDPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQ 129 L PFT V PL+I K +G +V D QG++Y++ ++GLWC++LG + R+++A + Sbjct: 16 LHPFTNLAAHPGVGPLVITKGDGIYVEDDQGKRYLEGMSGLWCSSLGFSHARVIEAGVEA 75 Query: 130 LNTLPFYHSFWNRTTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNA 189 + TLP+YH+F +R+ ++ LA++L+ M M+K FF NSGSEANDT VKLVWYY+NA Sbjct: 76 MRTLPYYHTFNHRSNPAAIMLAEKLVAMAPVP-MSKVFFANSGSEANDTAVKLVWYYHNA 134 Query: 190 LGRPNKKKFIARAKAYHGSTLISASLTGLPALHQNFDLPAPFVLHTDCPHYWRYHLPGET 249 +G+P+KKK IAR AYHG T+ +ASL+GL A H++FDLP +L CPH++RY PGE+ Sbjct: 135 IGKPDKKKIIARTNAYHGVTVAAASLSGLQANHRDFDLPIDRILRAGCPHHYRYGAPGES 194 Query: 250 EEEFSTRLAKNLEDLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILF 309 E F++RLA+ LE LI +GP+TI AFIAEPVMGAGGVI PPATYF +IQAV++++DIL Sbjct: 195 EAAFASRLAQELEALIQAQGPDTIGAFIAEPVMGAGGVIVPPATYFAEIQAVLRRHDILL 254 Query: 310 IADEVICAFGRLGTMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNK 369 IADEVIC FGR G MFGS Y ++PD++T AKALSS YMPI AV+VS +V I + S K Sbjct: 255 IADEVICGFGRTGAMFGSTTYGMRPDILTCAKALSSGYMPISAVMVSEKVHAAIAANSGK 314 Query: 370 LGSFSHGFTYSGHPVACAVALEAIKIYKERNMVERVNRISPKFQEGLKAFSDSPIIGEIR 429 +G+F HGFTYSGHPV AVALE +++Y++ +++ VN I+P+FQ+ L+A++ ++GE+R Sbjct: 315 IGTFGHGFTYSGHPVTTAVALETLRVYEDDRILDHVNAIAPRFQQALQAYAGRALVGEVR 374 Query: 430 GLGLILATEFANNKSPNDHFPPEWGVGAYFGAQCQKNGMLVRVAGDTIMMSPPFVVTPEE 489 G+GL+ A E A + F P G Q+ G++VR GDTI PP ++T + Sbjct: 375 GVGLLGAIELAAEPAARRAFDPALKAGPRLAQLAQEQGLIVRAMGDTIAFCPPLIITEAQ 434 Query: 490 LDELIRIYGKAL 501 + EL + +A+ Sbjct: 435 IGELFARFERAM 446 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: 544 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: 515 Length of database: 448 Length adjustment: 34 Effective length of query: 481 Effective length of database: 414 Effective search space: 199134 Effective search space used: 199134 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 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