Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS26240 Length = 420 Score = 226 bits (575), Expect = 1e-63 Identities = 150/403 (37%), Positives = 210/403 (52%), Gaps = 38/403 (9%) Query: 23 FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEP 82 F R E S LWD +G YIDFA GIAV GH HPRLV+A+ Q +F HT Y P Sbjct: 24 FYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPRLVQAMQAQMERFTHTA--YQIVP 81 Query: 83 V---LRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKN 136 + LA+++ FA + F +GAEA E A+K+AR + + G++AF Sbjct: 82 YASYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFSG 135 Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIY-------NDLDSAKAL-------ID 181 FHGRT+ ++ G+ Y F P P + HA Y + DS AL +D Sbjct: 136 GFHGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQDSINALHQLFKADVD 195 Query: 182 DN-TCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240 A+I EP+QGEGG A A+F+R LR +CD H LL+ DEVQTG GRTG+L+A H Sbjct: 196 PKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAMEH 255 Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300 Y VTPDL + AK+L GG P+ A+ G G TY GNPLA A A V + Sbjct: 256 YDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDVLE 315 Query: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGK-----AKAIS 355 + +++ Q ++L+ + +R E+RG+G +I + + G+ + + Sbjct: 316 SEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFR-KADGRPDPEFTRQVQ 374 Query: 356 NQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGLDRFELA 396 ++A E GL++L G NVVRF L I + ++ GL E A Sbjct: 375 DRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGILEAA 417 Lambda K H 0.321 0.137 0.412 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: 423 Number of extensions: 20 Number of successful extensions: 4 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: 406 Length of database: 420 Length adjustment: 31 Effective length of query: 375 Effective length of database: 389 Effective search space: 145875 Effective search space used: 145875 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