Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_092344193.1 BLU87_RS01675 acetylornithine transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_900107645.1:WP_092344193.1 Length = 397 Score = 342 bits (878), Expect = 9e-99 Identities = 173/370 (46%), Positives = 234/370 (63%), Gaps = 4/370 (1%) Query: 21 YAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNV 80 Y + G G + D G+ +DF G+AVN LGH HP +VAAL EQA KL H SN Sbjct: 19 YGRFPLVAASGKGCWLTDIDGKRYLDFLAGVAVNSLGHCHPKVVAALQEQAAKLLHCSNY 78 Query: 81 FTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNS 140 + + LA L + +F +RVFFCNSGAEANEAA KL R+ + D +GT+++EI+ A++S Sbjct: 79 YHIPQQIELAEILCEHSFGDRVFFCNSGAEANEAALKLVRKYSADTYGTDRFEIITAIDS 138 Query: 141 FHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPIQGEGG 200 FHGRTL T++ GQ + GF P I+G +VP+ D+AALK A+ KTCA+++EPIQGEGG Sbjct: 139 FHGRTLATISATGQDRIQSGFAPLISGFKYVPFGDIAALKTAIGPKTCAIMMEPIQGEGG 198 Query: 201 VLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGG 260 + YLQ ARELCD HN LL+FDE+Q G+GR+GKLFAY+H V PD++T AK+L G Sbjct: 199 INVPPQGYLQAARELCDKHNLLLIFDEIQVGLGRTGKLFAYEHDNVEPDVMTLAKALAAG 258 Query: 261 FPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKHDKFKT 320 PI AM+ E A L GTHG+T+GGNPL A A + V+ +++ A + K Sbjct: 259 PPIGAMIAREKYATALSPGTHGSTFGGNPLLTAAGVAAMKVLLEDHIIDNCVAMGNYLKA 318 Query: 321 RLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDVIRFAP 380 +LEQ+ KY +RG GL+LG L+ + +I A + GL+I V+RF P Sbjct: 319 QLEQLQNKYTFIKNIRGRGLILGMELT----FEGAEIVKTALQRGLLINCTAGKVLRFVP 374 Query: 381 SLVVEDADID 390 L+V +ID Sbjct: 375 PLIVTQDEID 384 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: 414 Number of extensions: 19 Number of successful extensions: 2 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: 397 Length adjustment: 31 Effective length of query: 375 Effective length of database: 366 Effective search space: 137250 Effective search space used: 137250 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