Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011033352.1 MM_RS07280 aspartate aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000007065.1:WP_011033352.1 Length = 395 Score = 264 bits (674), Expect = 4e-75 Identities = 160/384 (41%), Positives = 214/384 (55%), Gaps = 15/384 (3%) Query: 17 MVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWH 76 ++ Y + +G G+ V D G+E ID GIAVN +GH HP +V A+ QA KL H Sbjct: 26 VMQTYGRQPLVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAEKLIH 85 Query: 77 VSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVA 136 VSN++ E A L T E VFFCNSGAEA EAA KLAR T K VA Sbjct: 86 VSNLYYTEIQAEFAETLASITGMECVFFCNSGAEAVEAAMKLAR------VATGKSAFVA 139 Query: 137 ALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITH-VPYNDLAALKAAVSDKTCAVVLEPI 195 A +SFHGRT+ ++V +S Y D F P ++ T VPY+D A++ A+S+ T AVVLEPI Sbjct: 140 AEHSFHGRTIGALSVTHKSMYRDPFMPPVSSKTSFVPYSDADAIRKAISEDTAAVVLEPI 199 Query: 196 QGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAK 255 QGEGGV + YL+ RE+CD LL+FDEVQTG GR+G F + +GV PDI++ AK Sbjct: 200 QGEGGVNVPDPGYLKEVREICDETGTLLIFDEVQTGFGRTGTWFCKEQFGVEPDIMSMAK 259 Query: 256 SLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKH 315 ++GGGFP+ A+ L+ G H +T+GG PLACA A A I I ++L Sbjct: 260 AIGGGFPMGAIAARSGLS--FGRGQHASTFGGGPLACAAALASIQAIKEEKLLERSKEMG 317 Query: 316 DKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDV 375 F +L G EVRG GL++G + K + A G+++ V Sbjct: 318 AYFTKKLS--GMARDDIVEVRGKGLMIGVEI----KYPCGKFVDFAREHGVLVNCTSDSV 371 Query: 376 IRFAPSLVVEDADIDAGLDRFERA 399 +R P LV+ ID+ +D E+A Sbjct: 372 LRLVPPLVITKEQIDSVVDVLEQA 395 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: 384 Number of extensions: 19 Number of successful extensions: 5 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: 395 Length adjustment: 31 Effective length of query: 375 Effective length of database: 364 Effective search space: 136500 Effective search space used: 136500 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