Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_012170558.1 AZC_RS10525 aspartate aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000010525.1:WP_012170558.1 Length = 457 Score = 138 bits (347), Expect = 4e-37 Identities = 116/405 (28%), Positives = 188/405 (46%), Gaps = 45/405 (11%) Query: 33 GSRVWDQSGRELID-FAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFT--NEPALRL 89 G+ V D +G +ID FAG VN G+ ++V A +Q +L + + F+ +E A+RL Sbjct: 37 GAIVTDATGHSMIDGFAGLWCVNA-GYGVESIVEAAAKQMRELPYATGYFSLGSESAIRL 95 Query: 90 AHKLVDATFAE--RVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLF 147 A +L D + V+F G++A ++ + R H R +K + ++ + +HG + Sbjct: 96 AAELADRAPGDLNHVYFTLGGSDAVDSTVRFVRYYQHARGTPQKDQFISLASGYHGSSTV 155 Query: 148 TVNVGGQSKYSDGFGPKITGITHVPYN-----------------DLAALKAAVS----DK 186 + + GFG +P + +AAL+A V D+ Sbjct: 156 GAGLTALPLFHAGFGLPFDWQHKIPSHYAYRNPVGSDPAAIIAASVAALRAKVEEIGPDR 215 Query: 187 TCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGV 246 A EPIQG GGVL +++ RE+C + L V DEV TG GR+G LFA G+ Sbjct: 216 VAAFYAEPIQGSGGVLVPPDGWMKAMREVCRELDILFVADEVITGFGRTGPLFACTDEGI 275 Query: 247 TPDILTSAKSLGGGF-PIAAMLTTEDLAKHLVVGT------HGTTYGGNPLACAVAEAVI 299 PD++T+AK L G+ P+ A+ ++ + + G HG TY +P++ AV V+ Sbjct: 276 VPDLMTTAKGLTSGYVPMGAVFLSDHVYNTIADGAGESAVGHGYTYSAHPVSAAVGLEVL 335 Query: 300 DVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVL---------SDAW 350 + + NG A + L + + + L +VRG G+L L A Sbjct: 336 RLYEAGLLENGRRA-GARLMAGLRSLSD-HPLVGDVRGRGMLAAIELVTDKARKTPLPAA 393 Query: 351 KGKAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDR 395 + IF+ A GL+I ++ +AP L DADID ++R Sbjct: 394 ADPSHRIFDRAWDNGLVIRAFATGILGYAPPLCCTDADIDGIIER 438 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: 443 Number of extensions: 17 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: 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