Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Pf6N2E2_1623 Siderophore biosynthesis diaminobutyrate--2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1623 Length = 476 Score = 215 bits (548), Expect = 2e-60 Identities = 141/409 (34%), Positives = 219/409 (53%), Gaps = 47/409 (11%) Query: 7 YYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAV-P 65 Y R + + + YV D +GQ ++DC G + LGH +P + A+++ ++ + Sbjct: 46 YPRRIPLALQEAHGLYVRDTQGQLFMDCLAGAGTLALGHNHPVAIAAMRQTLDSGLPLHT 105 Query: 66 LNFATPARERFIEEFSKLLPPKFG----VVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFT 121 L+ TP ++RF+E+ LP F + F TG + +E A+K+A+ T + I++F+ Sbjct: 106 LDLTTPVKDRFVEDLFNALPENFARHARIQFCGPTGADGIEAALKLARTATGRKPILSFS 165 Query: 122 NSFHGRTMGSLSITWNEKYKKAFEPLYPHVRF--------------GKFNVP---HEVDK 164 +HG T+G+LS+ N K+A L V+F G+ V H +++ Sbjct: 166 GGYHGMTLGTLSLMGNLGPKQALGSLMADVQFLPYPYDYRCPFGIGGEAGVDAGLHFIEQ 225 Query: 165 LIGEDT------CCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRT 218 L+ + VVVE +QGEGGV PA +L+ LR+ ++ G LI DEVQTG GRT Sbjct: 226 LLSDPESGVLPPAAVVVEVVQGEGGVIPAPIRWLQGLRQLTRKFGVALIIDEVQTGLGRT 285 Query: 219 GAVWAFQKYGVEPDIFTAGKPVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAA 278 G ++AF+ +EPDI K + GGLP+ + V RE+ D ++PG H TF GN + MAA Sbjct: 286 GKLFAFEHADIEPDILVLSKAIGGGLPLAVMVYREEL-DTWKPGAHAGTFRGNQMAMAAG 344 Query: 279 AAASRLLREEDVPGRAERIGAELAKALGDTGSRLAV--RVKGMGLMLGLEL--------R 328 AA R + ED+PG A+ +G L AL R A +V+G GLM+G+E+ R Sbjct: 345 AATLRHIISEDLPGHADVMGQRLMAALRQLQDRYACLGQVRGRGLMVGVEIVSDTASDSR 404 Query: 329 V-KADQFIQPLLER-----GVMALTAGVN--TLRFLPPYMISKEDVEVV 369 V AD + ++R GV+ G + +RFLPP +I E+V+V+ Sbjct: 405 VPAADTALAQAIQRQCLRLGVILELGGRHGAVVRFLPPLIIQAEEVDVL 453 Lambda K H 0.320 0.138 0.408 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: 426 Number of extensions: 25 Number of successful extensions: 7 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: 383 Length of database: 476 Length adjustment: 32 Effective length of query: 351 Effective length of database: 444 Effective search space: 155844 Effective search space used: 155844 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 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