Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 332 bits (851), Expect = 2e-95 Identities = 189/483 (39%), Positives = 281/483 (58%), Gaps = 20/483 (4%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI G++ A + +TFE + P+ + +AR + D++ A+ AA RG W +SPA+ Sbjct: 22 FIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA--RGAWGRTSPAE 79 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R L ++AD +E + LA++ET+D GKPIR + D+P A R++A + G + Sbjct: 80 RSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGI 139 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + +A EP+GV+A I+PWNFPLL+ WKL PALAAGN VILKP+E++P+S + Sbjct: 140 SEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMV 199 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 L + + LP GVLNV+ GFG EAG+ L+++ I +AFTG T TG+ +++ A + N+ Sbjct: 200 LVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASE-NII 257 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIF----YNQGQVCIAGTRLLLEESIADEF 318 V LE GGKS NI FAD D A F NQG+VC +R L++E I D F Sbjct: 258 PVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRF 317 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA 378 + + + + G+PLDPAT +G + + S++ G +G +L G G A Sbjct: 318 MERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAG---GGRAD 374 Query: 379 IGPTI---------FVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAV 429 +GP + ++ + +EEIFGPVL VT F +E+AL++AND+ YGLGA V Sbjct: 375 VGPELAGGFYVQPTILEGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGV 434 Query: 430 WTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 WTR+ +RA+R R ++AG V+ N Y+ FGGYKQSG GR+ L+ + + K + Sbjct: 435 WTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQKTKNM 494 Query: 490 WIS 492 +S Sbjct: 495 LVS 497 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: 554 Number of extensions: 18 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: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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 Apr 09 2024. 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