Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_028311864.1 H566_RS0113545 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000482785.1:WP_028311864.1 Length = 489 Score = 499 bits (1286), Expect = e-146 Identities = 250/479 (52%), Positives = 328/479 (68%), Gaps = 4/479 (0%) Query: 19 ENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLS 78 + R FI+G+ AA F+ + PV + +A +AR + D+D A++AAR F+ W+ Sbjct: 11 DGRAFIDGKRVEAASGARFDCISPVDGSVIASVARCDAKDVDLAVAAARRAFDDRRWAGL 70 Query: 79 SPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKV 138 +PAKRK L + ADLM + LAL ETLD GKP++HS D+ GA IRWY EAIDK+ Sbjct: 71 APAKRKQTLVRFADLMVRERDALALTETLDMGKPLKHSRSADVMGAQNCIRWYGEAIDKI 130 Query: 139 YGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198 YGE+A T LA++ REPVGV+AA+VPWN+P+L+T WK+ PALAAGNSVILKPSEKSPL Sbjct: 131 YGEIAPTGDDALALVTREPVGVVAAVVPWNYPMLMTAWKIAPALAAGNSVILKPSEKSPL 190 Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258 SA+R+A LA EAG+P GV NV+ G+G EAG+AL+ H DID I FTGSTR GK++++ +G Sbjct: 191 SALRMAELALEAGIPAGVFNVLPGYGQEAGEALALHMDIDCIGFTGSTRVGKRIVECSGR 250 Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 SN+KR W E GGKS NIV AD DL A A+ IFYNQG+ C A +RLL+E SI D F Sbjct: 251 SNLKRAWTELGGKSPNIVCADVADLDAAVEASIGSIFYNQGESCNAPSRLLVEASIRDAF 310 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA 378 + ++P PLD T MG L+D +V +I G+++G L+ G Sbjct: 311 IEKALALVPRYEPADPLDMGTVMGALVDEGQLRTVMGYIEAGKAEGAALIAGGEQARIET 370 Query: 379 IG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDL 434 G PTIF V + ++REEIFGPVL V F A+ AND+ YGL AA+WTRD+ Sbjct: 371 GGYYVRPTIFAGVRNDMRIAREEIFGPVLSVIAFDDIADAVAQANDTSYGLHAAIWTRDI 430 Query: 435 SRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 S+AHR++R L+AG+V VN+Y++ D+TVPFGG+KQSGNGRDKSLHA EK+ E+KT W+ + Sbjct: 431 SKAHRVARALRAGTVHVNSYDEDDITVPFGGFKQSGNGRDKSLHAFEKYMEVKTTWVRI 489 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: 628 Number of extensions: 19 Number of successful extensions: 2 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: 489 Length adjustment: 34 Effective length of query: 461 Effective length of database: 455 Effective search space: 209755 Effective search space used: 209755 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