Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_066609126.1 V473_RS20290 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_001046645.1:WP_066609126.1 Length = 462 Score = 144 bits (362), Expect = 7e-39 Identities = 123/418 (29%), Positives = 195/418 (46%), Gaps = 57/418 (13%) Query: 19 APAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQ------AGKFW 72 A A + G+G L D +G+E ID G+ +G+ + +A EQ A ++ Sbjct: 29 AHGALLLESGKGMWLKDVEGRELIDAFAGLWCVNVGYGQDSIAEAAAEQMRRLPYATGYF 88 Query: 73 HTGNGYTNEPVLRLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGS-EKS 129 H G+ EP ++LA+QL+D + D V+F G++A ++A++ Y H+ G EK Sbjct: 89 HFGS----EPAVKLAQQLVDLSPEGLDHVYFTLGGSDAVDSAIRYITHY-HNAIGKPEKK 143 Query: 130 GIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYN------DLDSAKALI--- 180 +A + +HG + + + F LP + QH I + DL+ A I Sbjct: 144 QFIALERGYHGSSSTGAGLTALANFHRGF-DLPLRWQHHIASPYPYRSDLEGDDAAIIAR 202 Query: 181 -------------DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQT 227 DN A EP+QG GGV+ +L+ +RE C + L + DEV T Sbjct: 203 SVQELKDKVAQLGADNVAAFFCEPIQGSGGVIVPPVGWLKAMRETCTQLDILFVTDEVIT 262 Query: 228 GVGRTGELYAYMHYGVTPDLLSTAKALGGGF-PIGALLASER--------CASVMTVGTH 278 G GRTG ++A GVTPDL++ AK L G+ P+GALL S + A + +G H Sbjct: 263 GFGRTGPMFACEAEGVTPDLMTLAKGLTAGYVPMGALLMSGKVYEGIANGAAPEVAIG-H 321 Query: 279 GTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLL 338 G TY G+P++ AV EV +L ++ F L + A + + + RG GLL Sbjct: 322 GATYSGHPVSAAVGLEVLRLYTDGGILANGQRVATRFDAGLAGL-ANHPMVGDTRGRGLL 380 Query: 339 IGCVLKDEYAGKAK---------AISNQAAEEGLMILIAGANVVRFAPALIISEDEVN 387 L + KA+ + +A + G++ N++ APAL S+ E++ Sbjct: 381 GAIELVADKGSKARFDPGLKLADRLFAKAYDNGVIFRAFADNIIGLAPALCASDGEMD 438 Lambda K H 0.321 0.137 0.412 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: 496 Number of extensions: 33 Number of successful extensions: 6 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: 462 Length adjustment: 32 Effective length of query: 374 Effective length of database: 430 Effective search space: 160820 Effective search space used: 160820 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: 51 (24.3 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