Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000504245.1:WP_034272173.1 Length = 393 Score = 302 bits (773), Expect = 1e-86 Identities = 176/390 (45%), Positives = 231/390 (59%), Gaps = 24/390 (6%) Query: 17 MVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWH 76 M+ NY A VRG G+ V+D G +D GGIAVN LGHAHPA+V A++EQ L H Sbjct: 11 MMDNYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGH 70 Query: 77 VSNVFTNEPALRLAHKLVD-ATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIV 135 SN++ N AL LA L+D A + +V FCNSGAEA EAA K+ R T K ++V Sbjct: 71 TSNLYINPVALSLAETLLDIAGLSGKVLFCNSGAEAVEAAIKITRL-------TGKSKLV 123 Query: 136 AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPI 195 A FHGRT+ ++V GQ + F P + G+THVP+ D AAL++AV T AV +EP+ Sbjct: 124 ACDGGFHGRTMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPV 183 Query: 196 QGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAK 255 GEGGV+PA +L+ ARE+ A ALLV DEVQTG+GR G FA+Q GVTPD++T AK Sbjct: 184 LGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAK 243 Query: 256 SLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKH 315 LGGG P+ A++ + L G HGTT+GGNP+ACA AVI I +L+ V Sbjct: 244 GLGGGLPLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLG 303 Query: 316 DKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDV 375 + ++ + L +EVRG GLL G L+ K A + AA+R G +I PDV Sbjct: 304 KDLAAGVRKL--DHPLVSEVRGAGLLQGIGLT---KPVAPTVATAAQRAGYLINPVQPDV 358 Query: 376 IRFAPSLVVED-----------ADIDAGLD 394 IR AP L++ + A +D GLD Sbjct: 359 IRLAPPLIITERQVADFLAALPAALDVGLD 388 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: 447 Number of extensions: 26 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: 393 Length adjustment: 31 Effective length of query: 375 Effective length of database: 362 Effective search space: 135750 Effective search space used: 135750 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 Jul 26 2024. The underlying query database was built on Jul 25 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