Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 275 bits (704), Expect = 2e-78 Identities = 178/477 (37%), Positives = 267/477 (55%), Gaps = 19/477 (3%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80 RL ++G+ A AE TF +DP T P A + D+D A++AAR F W+ + Sbjct: 5 RLIVDGKPLAMAE--TFPVIDPATGRPFADAPLASTADLDAAVAAARRAFP--GWAATPI 60 Query: 81 AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGA---ARAIRWYAEAIDK 137 R A + +AD +EA +ELA L + + GKP+ +++ +I GA ARA A+D Sbjct: 61 EDRAAAILAIADSIEAAKDELARLLSAEQGKPVPNAV-GEIMGALAWARATAGLRPAVD- 118 Query: 138 VYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSP 197 V + R+P+GV+A+I PWNFP+++ W + P L AGN+V++KPS +P Sbjct: 119 ----VLKDDDSVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTP 174 Query: 198 LSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAG 257 L+A+R+ +A A LP GVLN VTG E G+A++ H ID I FTGST TG+ ++ D G Sbjct: 175 LAALRMVEIAN-AHLPPGVLNSVTG-EVEIGRAIASHPGIDKIVFTGSTPTGRSIMAD-G 231 Query: 258 DSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317 +N+KR+ LE GG A IV D D+ + A+ A F N GQ+C A R+ + ESI D Sbjct: 232 AANLKRLTLELGGNDAAIVLPDA-DVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDA 290 Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA--GL 375 L + A+ G D A+ G + + D V + + + G L G A G Sbjct: 291 LAEKLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGD 350 Query: 376 AAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435 ++ VDV + EE FGP+L V R++ E AL AN ++ GLG +VW+ D + Sbjct: 351 GYFFPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPA 410 Query: 436 RAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492 A ++RL+AG+V+VN++ VPFGG KQSG G + L+ LE++ +L+T+ ++ Sbjct: 411 AALAFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRVA 467 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: 573 Number of extensions: 25 Number of successful extensions: 8 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: 469 Length adjustment: 34 Effective length of query: 461 Effective length of database: 435 Effective search space: 200535 Effective search space used: 200535 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: 52 (24.6 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