Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_015929538.1 MNOD_RS13870 aspartate aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000022085.1:WP_015929538.1 Length = 457 Score = 146 bits (368), Expect = 1e-39 Identities = 126/409 (30%), Positives = 195/409 (47%), Gaps = 47/409 (11%) Query: 33 GSRVWDQSGRELID-FAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFT--NEPALRL 89 G+ V D +GREL+D FAG VN G+ H ++V A Q +L + + F +EPA+RL Sbjct: 37 GATVTDAAGRELLDGFAGLWCVNA-GYGHDSIVEAAARQMRELPYATAYFGLGSEPAIRL 95 Query: 90 AHKLVDATFAE--RVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLF 147 A L + + V+F G++A + +L R R EK + ++ +HG + Sbjct: 96 AAALAERAPGDLNHVYFTLGGSDAVDTTVRLIRNYQTVRGKPEKDQFISLEQGYHGSSTV 155 Query: 148 TVNVGGQSKYSDGFG-----------------PKITGITHVPYNDLAALKAAVSD----K 186 + + FG P + + + LAAL+A V + + Sbjct: 156 GAGLTALPAFHANFGLPFAWQHKIPSPYPYRNPAGSDLEAIIAASLAALRAKVEELGPER 215 Query: 187 TCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGV 246 A EPIQG GGV+ +++ R+LC + L V DEV TG GR+G LFA V Sbjct: 216 VAAFYAEPIQGSGGVIVPPRGWMKAMRDLCAELDILFVADEVITGFGRTGPLFACTEDEV 275 Query: 247 TPDILTSAKSLGGGF-PIAAML-------TTEDLAKHLVVGTHGTTYGGNPLACAVAEAV 298 PD++T+AK L G+ P+ A+ T D A +G HG TY +P++ AV V Sbjct: 276 VPDLMTTAKGLTSGYVPMGAVFLSNRIYDTIADGAGEAAIG-HGYTYSAHPVSAAVGLEV 334 Query: 299 IDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLL--LGCVLSDAWKG---- 352 + + + NG A + + L+ + + + L +VRG GLL L V+ A K Sbjct: 335 LRLYENGLLENGRRA-GTRLQAGLQSLAD-HPLVGDVRGRGLLAALELVVDKARKAPLPA 392 Query: 353 ---KAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFER 398 A+ IF+ A GL+I G ++ +AP L +A+IDA ++R R Sbjct: 393 AADPARRIFDRAWNNGLVIRAFGNGILGYAPPLCCTEAEIDAIVERTRR 441 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: 468 Number of extensions: 28 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: 457 Length adjustment: 32 Effective length of query: 374 Effective length of database: 425 Effective search space: 158950 Effective search space used: 158950 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 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