Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011911296.1 PST_RS00235 aspartate aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000013785.1:WP_011911296.1 Length = 439 Score = 151 bits (382), Expect = 3e-41 Identities = 115/397 (28%), Positives = 181/397 (45%), Gaps = 38/397 (9%) Query: 30 RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEPA-LR 88 R G GR+++D G+ GH + A+++Q ++ P Sbjct: 31 RAEGMYYTASDGRQVLDGTAGLWCCNAGHGRREISEAVSKQIARMDFAPTFQMGHPLPFE 90 Query: 89 LAHKL--VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTL 146 LA KL + RVFF NSG+E+ + A K+A + ++ ++HG Sbjct: 91 LAEKLAAISPEGLNRVFFTNSGSESADTALKIALAYQRAIGQGSRTRLIGRELAYHGVGF 150 Query: 147 FTVNVGGQSKYSDGFGPKITGITHVPYN-DLA-----------------ALKAAV----S 184 ++VGG + FGP + G+ H+P+ DL L+ V + Sbjct: 151 GGMSVGGMANNRRAFGPMLPGVDHLPHTLDLQRNAFSKGLPQHGVERADELERLVTLHGA 210 Query: 185 DKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHY 244 + AV++EP+ G GV+ + YLQ RE+ H LL+FDEV TG GR G+ FA Q + Sbjct: 211 ENIAAVIVEPMSGSAGVILPPVGYLQRLREITAKHGILLIFDEVITGFGRVGEAFAAQRW 270 Query: 245 GVTPDILTSAKSL-GGGFPIAAMLTTEDLAKHLVVGT-------HGTTYGGNPLACAVAE 296 GVTPDILT AK L G P+ A+ + L + G HG TY G+P+ACA A Sbjct: 271 GVTPDILTCAKGLTNGAIPMGAVFVADRLYDAFMQGPESVIEFFHGYTYSGHPVACAAAL 330 Query: 297 AVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAK- 355 A + + ++ L + + + ++R +GL+ G + G K Sbjct: 331 ATQQIYQQENLFQKAIDLEPYWQEALFSLRDLPNVI-DIRTVGLVAGIQFAAHADGVGKR 389 Query: 356 --DIFNAAEREGLMILQAGPDVIRFAPSLVVEDADID 390 ++F GL++ +G D I +P+L+VE A+ID Sbjct: 390 GYEVFRECFENGLLVRASG-DTIALSPALIVEKAEID 425 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: 428 Number of extensions: 23 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 439 Length adjustment: 32 Effective length of query: 374 Effective length of database: 407 Effective search space: 152218 Effective search space used: 152218 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 Apr 09 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