Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_067911749.1 AQZ52_RS13615 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_001519075.1:WP_067911749.1 Length = 486 Score = 285 bits (730), Expect = 2e-81 Identities = 188/460 (40%), Positives = 257/460 (55%), Gaps = 11/460 (2%) Query: 36 TFETVDPVT-QAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLM 94 TFET P LA IARG + A AA F W+ + A+R L++LADL+ Sbjct: 28 TFETRCPFEWDRKLADIARGDAQTAALAAEAASAAFPA--WAALTAAERGVYLHRLADLI 85 Query: 95 EAHAEELALLETLDTGKPIRH-SLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMI 153 EA+ E+LA++E LD G + LR + GAA R YA+ + + E +S L + Sbjct: 86 EANVEKLAVVECLDMGMLLESLRLRVILRGAAN-FRTYAD-LAAHHEERVWSSRGTLNRV 143 Query: 154 VREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLP 213 +R P G I PWN P +L+ WK PALAAGN+VILKP++ SPLSA LA L EAG+P Sbjct: 144 IRMPAGPALIITPWNAPFMLSTWKCAPALAAGNTVILKPADWSPLSASVLADLIHEAGIP 203 Query: 214 DGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSA 273 GV N+V G G E G AL+ I I+FTGS T + + + A + N+ E GGKS Sbjct: 204 AGVFNIVQGLGAELGNALTSDPRIKRISFTGSVPTARVIGRAAAE-NIVPFTAELGGKSP 262 Query: 274 NIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGH 333 +VFAD D+ AA+ AAG F + GQVC+AGTR+++EES+ + FL G Sbjct: 263 LLVFADA-DI-DAAAKKAAGQFDDSGQVCMAGTRIIVEESVKEAFLEKFHGYTDAHVMGD 320 Query: 334 PLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA--IGPTIFVDVDPNA 391 DPATTM LI HA+ V FI + G ++ G A I PT+ V D + Sbjct: 321 SRDPATTMSALIHPVHAERVLGFIDRARAAGDTVVRGGKRWKEGANWIEPTLIVPKDNQS 380 Query: 392 SLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFV 451 + + E+FGPVL F E + + LAN + YGL V+T RA R+ R ++ G+V+V Sbjct: 381 EVVQNEVFGPVLTFQTFRDEAEGVALANSTAYGLSGIVYTGSEDRAQRVGRAVRGGTVWV 440 Query: 452 NNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 N + D+T PFGG SG GR+ +AL+ ++LKT+ I Sbjct: 441 NTFLVRDLTAPFGGIGISGIGREGGDYALDFHSDLKTLQI 480 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: 597 Number of extensions: 27 Number of successful extensions: 5 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: 486 Length adjustment: 34 Effective length of query: 461 Effective length of database: 452 Effective search space: 208372 Effective search space used: 208372 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 24 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