Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Dyella79:N515DRAFT_4224 Length = 456 Score = 130 bits (328), Expect = 7e-35 Identities = 121/398 (30%), Positives = 182/398 (45%), Gaps = 23/398 (5%) Query: 98 AEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREP 157 A+E LLE + IRH+L A RW G + + +E+ +P Sbjct: 47 AQETDLLEVFPSLSAIRHAL-------AHGRRWMKPRRSWP-GLLFMPARNEIRP---QP 95 Query: 158 VGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVL 217 +GV+ IVPWN+PL L + ALAAGN V++K SE +P + A LA P+ V Sbjct: 96 LGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYTPQFSALFAQLAARYFKPEEVC 155 Query: 218 NVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVF 277 VVTG + QA S D + FTGST G+ +++ A +N+ V LE GGKS IV Sbjct: 156 -VVTG-DADVAQAFSA-LPFDHLLFTGSTAVGRHVMR-AASANLTPVTLELGGKSPAIV- 210 Query: 278 ADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDP 337 A G +N GQ CIA +LL + DEF+A + A P P+ Sbjct: 211 GPGARFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAAARDVAARLYP-QPVRN 269 Query: 338 ATTMGTLIDCAH---ADSVHSFIREGESKGQLLLDGRNAGLAAAIGPTIFVDVDPNASLS 394 + + + A R+G +K LL D + + P + V + ++ Sbjct: 270 EQYASIISERQYQRLAALRDDAARDG-AKLTLLGDETDDIQRRRMTPALLTGVSESMAVM 328 Query: 395 REEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNN- 453 +EEIFGP+L + + EQA+ + L ++ D + R+ R AG V +N+ Sbjct: 329 QEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGALVDRVLARTTAGGVTINDT 388 Query: 454 -YNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490 Y+ +PFGG SG+G F+ LK+++ Sbjct: 389 LYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLKSVF 426 Lambda K H 0.317 0.133 0.389 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: 493 Number of extensions: 23 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: 495 Length of database: 456 Length adjustment: 33 Effective length of query: 462 Effective length of database: 423 Effective search space: 195426 Effective search space used: 195426 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: 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