Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= BRENDA::P23883 (495 letters) >MicrobesOnline__882:208821 Length = 464 Score = 171 bits (432), Expect = 7e-47 Identities = 135/424 (31%), Positives = 197/424 (46%), Gaps = 12/424 (2%) Query: 73 GDWSLSSPA-KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWY 131 GD + PA +R A+L +LA LM HAE L + GKP S+ + + A +RW Sbjct: 38 GDPAHRIPAHERLAILERLATLMRTHAEALVRDAVREGGKPWADSVVE-VERAIDGVRWA 96 Query: 132 AEAIDKVYGE-----VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186 A + ++ G + S+ LA VREP GV+ AI +N P+ L + PA AAG Sbjct: 97 ARELAQLGGREVPMGLTPASAGRLAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGC 156 Query: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246 V++KP+ +PLS + L EAG+P+ ++ A + L + ++F GS+ Sbjct: 157 PVLVKPASATPLSCRNVLRLMHEAGVPEAWATMLPCAAATA-EKLVADPRVAFLSFIGSS 215 Query: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306 R G L LE GG +A +V DL A G FY+ GQVC++ Sbjct: 216 RVGWHLRSKLAPG--ATCALEHGG-AAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQ 272 Query: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366 R+ A F L A G P+ T +G LID VH ++ E + G Sbjct: 273 RVFAPHETARTFAERLAAAAAQLPTGDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGT 332 Query: 367 LLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLG 426 +L G PT+ D L+R E+FGPV+ V ++A+ AND + Sbjct: 333 VLCGGAPLSETLYSPTVVYDPPQGCRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQ 392 Query: 427 AAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMT-VPFGGYKQSGNGRDKSLHALEKFTE 485 AAV+ RD+ A +RRL A V VN++ + +PFGG +SG G A+ + T Sbjct: 393 AAVFARDVDVALDTARRLNATGVMVNDHTAFRVDWMPFGGRGESGMGTGGIGPAMHEMTT 452 Query: 486 LKTI 489 K I Sbjct: 453 EKLI 456 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: 545 Number of extensions: 28 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: 464 Length adjustment: 34 Effective length of query: 461 Effective length of database: 430 Effective search space: 198230 Effective search space used: 198230 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