Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_028949958.1 Q385_RS0101465 aspartate aminotransferase family protein
Query= reanno::Btheta:353284 (373 letters) >NCBI__GCF_000619805.1:WP_028949958.1 Length = 457 Score = 119 bits (297), Expect = 2e-31 Identities = 120/432 (27%), Positives = 196/432 (45%), Gaps = 85/432 (19%) Query: 16 KGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINK----- 70 K +G ++D G +YLDL ++ + G+ + + I NQ+ TLG ++ + K Sbjct: 31 KSEGSYLYDLEGKQYLDLQMWYSACNFGYNNKRINDGIKNQMDTLGQLASQFLTKEKILL 90 Query: 71 ---LQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRT 127 + + V +R K+ G +++ G++A E++LK+ Y + +F +HGRT Sbjct: 91 SYKIAKSVEDRF-KVKGRVHFNV----GGSQAIEDSLKIVRNYTKKNLNFAFMGGYHGRT 145 Query: 128 SLAVEATNNPTIIAPINNNGHVT----YLPL---------NDIEAMKQELAKG------- 167 + ATN + GH + ++P D E AK Sbjct: 146 ---IGATNITSSYRYRERYGHFSDRAFFIPFPYCFRCPYGKDKETCDLYCAKEFEKLFES 202 Query: 168 ---DVC----------AVIIEGIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGY 214 VC A IE IQG GG IP ++ ++++ V E +L+ DEIQ G+ Sbjct: 203 EYYTVCNPKTKNCEFGAFYIEPIQGTGGYIIPPKDYFKKIKPVLDEYKVLLVSDEIQMGF 262 Query: 215 GRSGKFFAHQYNHIQPDIITVAKGIGNGF-PMAGV-----LISP-MFKPVYGQLGTTFGG 267 R+GK ++ ++ + PDII K + NG P++G+ LI+P +F P G +TF Sbjct: 263 YRTGKLWSIEHFGVVPDIIVFGKSLTNGMNPLSGLWAKEELINPEIFPP--GSTHSTFSS 320 Query: 268 NHLACSAALAVMDVIEQDNLVENAKAVGD----YLLEELKKFPQIKEVRGRGLMIGLEFE 323 N + A L V +IE+ + + K G+ YL + KK+P I +V G GL + +E Sbjct: 321 NPIGVRAGLEVFKIIEEKDYEKIVKEKGEKFLNYLKDLKKKYPFIGDVDGLGLALRVEIC 380 Query: 324 E-----PIKELRSRLI--------------YDEHVFTGASGTNVLRLLPPLCLSMEE--- 361 E P K+L +++ Y + G NVL L P L ++ EE Sbjct: 381 EKDGYTPSKKLTDKIVEEGLKANLNLNEKTYGLVLDVGGYYKNVLTLAPSLDITDEEINL 440 Query: 362 ADEFL-ARFKRV 372 A EFL +F R+ Sbjct: 441 AVEFLDIQFSRI 452 Lambda K H 0.320 0.139 0.403 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: 410 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 373 Length of database: 457 Length adjustment: 31 Effective length of query: 342 Effective length of database: 426 Effective search space: 145692 Effective search space used: 145692 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 10 2024. The underlying query database was built on Apr 09 2024.
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