Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >FitnessBrowser__Dyella79:N515DRAFT_4224 Length = 456 Score = 145 bits (365), Expect = 4e-39 Identities = 108/343 (31%), Positives = 165/343 (48%), Gaps = 14/343 (4%) Query: 156 EPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKG 215 +P+GVVG IVPWN+PL +A + AL+ GN V++K SE +P + A+LA P+ Sbjct: 94 QPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYTPQFSALFAQLAARYFKPEE 153 Query: 216 VLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNI 275 V V+ G AL D L+FTGST + + ++ + +N+ V LE GGKSP I Sbjct: 154 VC-VVTGDADVAQAFSAL--PFDHLLFTGSTAVGRHVM-RAASANLTPVTLELGGKSPAI 209 Query: 276 VFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPL 335 V A +A E FN G+ C A +L+ R+ D+F+ + P Sbjct: 210 VGPGA-RFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAAARDVAARLYP---- 264 Query: 336 DPATN--VGALVDTQQMNTVLSYIESGHADGARLVAGGKRTLQETGGTYVEPTIFDGVSN 393 P N +++ +Q + + + DGA+L G T + + P + GVS Sbjct: 265 QPVRNEQYASIISERQYQRLAALRDDAARDGAKLTLLGDET-DDIQRRRMTPALLTGVSE 323 Query: 394 AMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADISKAHLTARALRAGSV 453 +M + QEEIFGP+L ++ +D E+AIA P+ LA ++ D + AG V Sbjct: 324 SMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGALVDRVLARTTAGGV 383 Query: 454 WVNQ--YDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATW 494 +N Y PFGG SG+G F ++ LK+ + Sbjct: 384 TINDTLYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLKSVF 426 Lambda K H 0.316 0.132 0.390 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: 520 Number of extensions: 27 Number of successful extensions: 6 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: 497 Length of database: 456 Length adjustment: 33 Effective length of query: 464 Effective length of database: 423 Effective search space: 196272 Effective search space used: 196272 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 (21.6 bits) S2: 51 (24.3 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