Align 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase; AONS/AKB ligase; 7-keto-8-amino-pelargonic acid synthase; 7-KAP synthase; KAPA synthase; 8-amino-7-ketopelargonate synthase; Alpha-oxoamine synthase; Glycine acetyltransferase; EC 2.3.1.29; EC 2.3.1.47 (characterized)
to candidate GFF2001 PGA1_c20350 5-aminolevulinate synthase HemA
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Phaeo:GFF2001 Length = 409 Score = 228 bits (580), Expect = 3e-64 Identities = 139/405 (34%), Positives = 213/405 (52%), Gaps = 11/405 (2%) Query: 1 MSLDLRARVREELERLKREGLY-----ISPKVLEAPQEPVTRVEG--REVVNLASNNYLG 53 M +D A++ + +++L EG Y I + + P TR +G +++ N+YLG Sbjct: 1 MPVDYTAKLDQAIDQLHTEGRYRTFIDIERQNGQFPHAVWTRPDGSKQDITVWCGNDYLG 60 Query: 54 FANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTA 113 HP + E ++ GAGSG R I+GT YH +LE LA E+AL+ S + A Sbjct: 61 MGQHPVVLEAMHGAIDATGAGSGGTRNISGTTVYHKQLEAELADLHQKEAALLFTSAYIA 120 Query: 114 NQGVLGALLK--EGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDG 171 N L L K G ++FSD LNHAS+I+G+R + +FRH DVAHL ELL A D Sbjct: 121 NDATLSTLPKLFPGLIIFSDALNHASMIEGVRRNGGAKRIFRHNDVAHLRELLAAADPAA 180 Query: 172 LKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQD 231 KLI + V+SMDGD P+ +I LA+++ A+ Y+D+ H G+ G +G G G Sbjct: 181 PKLIAFESVYSMDGDFGPIAEICDLAEEFGALTYIDEVHAVGMYGARGGGVTERDGLIDR 240 Query: 232 PDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEK 291 D+V TL+KA+ +GGY A + ++ D + + A F+F+TS PAV ++ ++ Sbjct: 241 IDIVN-GTLAKAYGVMGGYIAASAKMCDAIRSYAPGFIFTTSLAPAVAAGAAASVAYLKT 299 Query: 292 EPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLL-EEGVFAV 350 PE E+ R K L LG + + I PV+ G + S +LL + G++ Sbjct: 300 APELREQHQLQARILKMRLKGLGLPIIDHGSHIVPVIVGNPVHTQKLSDMLLSDHGIYVQ 359 Query: 351 GIGFPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVGKRLGIIR 395 I FPTVPRG R+R + H + +D ++A + + + R Sbjct: 360 PINFPTVPRGTERLRFTPSPVHGPKEIDALVKAMDALWSHCALNR 404 Lambda K H 0.319 0.137 0.394 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: 336 Number of extensions: 21 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: 395 Length of database: 409 Length adjustment: 31 Effective length of query: 364 Effective length of database: 378 Effective search space: 137592 Effective search space used: 137592 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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