Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Dyella79:N515DRAFT_1410 Length = 381 Score = 169 bits (428), Expect = 1e-46 Identities = 118/359 (32%), Positives = 183/359 (50%), Gaps = 16/359 (4%) Query: 34 VALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTPE- 92 V L G PDF+ P+ ++EA RA+A+G+ +YAP G+P LRE +A K R G + Sbjct: 28 VNLGQGFPDFEPPQALREAIARAMAEGRNQYAPGIGLPTLREQIALKTERMYGRRIDAAG 87 Query: 93 ETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVE-TLPEEGFV 151 E VT G +ALF A++ GDEVIV P + SY ++ G V + T+P G Sbjct: 88 EVTVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYEPVIELQGAKAVHIPLTVPSFGV- 146 Query: 152 PDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLY 211 D +RVR A+TPRT+ +++NSP+NP+GAV L+ LA + + + ++SDE+YEH+++ Sbjct: 147 -DWQRVRDAVTPRTRMILINSPHNPSGAVLSAADLDQLAAIVRDTEIVVLSDEVYEHIVF 205 Query: 212 EGE-HFSPGRVA--PEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPD 268 +G H S R A ++ V+ K + TGW++GYA P + V T Sbjct: 206 DGALHQSVLRHAELAARSIVVSSFGKTYHCTGWKLGYAVAPAALSAEFRKVHQYLTFCTF 265 Query: 269 TIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTS 328 AQ A E + + ++E+ Y+ +RD + K + G ++ L+D S Sbjct: 266 HPAQVAFAEFMAS--TPEHYLELP-AFYQAKRDRFRALIAPSRFKLLDVPGGYFQLVDYS 322 Query: 329 PI--APDEVRAAERLLEAGVAVVPGTDFAAFGH----VRLSYATSEENLRKALERFARV 381 I PD + + GVA +P F VRL +A S+ + A ER ++ Sbjct: 323 AIRDEPDVTFCEWLVKQGGVAAIPLAPFYETAPDTRLVRLCFAKSDATMDAAAERLCKL 381 Lambda K H 0.317 0.133 0.379 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: 337 Number of extensions: 19 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: 385 Length of database: 381 Length adjustment: 30 Effective length of query: 355 Effective length of database: 351 Effective search space: 124605 Effective search space used: 124605 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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