Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_001584165.1:WP_128083232.1 Length = 420 Score = 226 bits (577), Expect = 7e-64 Identities = 151/408 (37%), Positives = 210/408 (51%), Gaps = 33/408 (8%) Query: 26 FIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNE 84 F S +WD GR IDFA GIAV GH HP LVAA+ EQ K H + + Sbjct: 19 FYASHALNSEIWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFTHTAYQIVPYG 78 Query: 85 PALRLAHKLVDAT---FAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSF 141 + LA ++ T A++ F ++GAEA E A K+AR T + ++A +F Sbjct: 79 SYVELAERINAVTPGDHAKKTTFFSTGAEAVENAVKIARAA------TGRSAVIAFSGAF 132 Query: 142 HGRTLFTVNVGGQS-KYSDGFGPKITGITHVPY----------NDLAAL----KAAVSDK 186 HGRT+ + + G+ Y GFGP + HVP+ N LAAL KA V K Sbjct: 133 HGRTMMGMALTGKVVPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAALQSLFKADVDPK 192 Query: 187 -TCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYG 245 A++LEP+QGEGG A +++Q R+LCD H LLV DEVQTG R+GKLFA +H G Sbjct: 193 RVAAIILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEHSG 252 Query: 246 VTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTP 305 V PD++T AKSL GG P++A+ ++ G G TY GNPLA A A AV+DVI Sbjct: 253 VIPDLMTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVASALAVLDVIEEE 312 Query: 306 EVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGK-----AKDIFNA 360 +++ N + K LE + ++RGLG ++ + + K + Sbjct: 313 KLVERANVLGGRLKQVLEGLRADVPQIADIRGLGAMVAVEFTQPGSKQPDADFTKKVQAE 372 Query: 361 AEREGLMILQAG--PDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406 A + GL++L G + IRF L +EDA +D L +A + A Sbjct: 373 ALKNGLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAMRTVAAA 420 Lambda K H 0.320 0.136 0.400 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: 427 Number of extensions: 19 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: 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 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