Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 309 bits (792), Expect = 1e-88 Identities = 179/476 (37%), Positives = 269/476 (56%), Gaps = 17/476 (3%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80 + +I+G++ + A T E P A LA + +G + D D+A++AARG F+ WS++ Sbjct: 6 QFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDA--WSVTPA 63 Query: 81 AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140 A+R A L K+ + ++A A+E+A TL+ G P + S R + + Y++ + Sbjct: 64 AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPF 123 Query: 141 EVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200 E +S +VRE VGV+AAI PWN+PL K+ ALAAG +V+LKPSE +PL+A Sbjct: 124 EEKVGNSK----VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNA 179 Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260 LA + AG+P GV N++TG+G G+A+ H ++D ++FTGSTR G + + + + Sbjct: 180 FLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTR-VSELASAT 238 Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320 +KRV LE GGKSA I+ D D A + N GQ C A TR+L+ + E Sbjct: 239 VKRVALELGGKSAAIILDDA-DFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAK 297 Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIG 380 L + AQ ++ G P+ T+G L D V +I +G ++G LL G A L + Sbjct: 298 LAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTG-GADLPEGVN 356 Query: 381 -------PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRD 433 PTIF V P++S+++EEIFGPVL + + EE A+ +AN + YGL VW+ Sbjct: 357 PDGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSAT 416 Query: 434 LSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 A +++RR++ G V +N +M PFGGYKQSGNGR+ + LE F E K + Sbjct: 417 DEHAEQVARRMRTGQVEING-GTFNMYAPFGGYKQSGNGRELGKYGLEDFLEFKAM 471 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: 515 Number of extensions: 22 Number of successful extensions: 7 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: 479 Length adjustment: 34 Effective length of query: 461 Effective length of database: 445 Effective search space: 205145 Effective search space used: 205145 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