Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 323 bits (828), Expect = 9e-93 Identities = 187/481 (38%), Positives = 273/481 (56%), Gaps = 16/481 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI G++ A A+ F+ P+ + +IAR +++DI+RA+ AA + W+ +S A Sbjct: 22 FIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAA--KAGWARTSAAD 79 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L ++AD ME + LA ET D GKPIR +L DIP A R++A + G + Sbjct: 80 RSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLRSQEGSI 139 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + +A EP+GV+ I+PWNFPLL+ CWKL PALAAGN V+LKP+E++P S + Sbjct: 140 SEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIMV 199 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 A + + LP GVLN+V GFG EAG+ L+ I IAFTG T TG+ +++ A N+ Sbjct: 200 WAEMIGDL-LPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAA-QNLI 257 Query: 263 RVWLEAGGKSANIVFADC----PDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 V LE GGKS NI F D D A NQG+VC +R L++ESI ++F Sbjct: 258 PVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFALNQGEVCTCPSRALVQESIYEKF 317 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA 378 + ++ G PLDPAT +G + + ++ G ++G LL G + Sbjct: 318 MERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRKILPG 377 Query: 379 -------IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 + PT+F + + +EEIFGPVL VT F +EE+AL++AND+ +GLGA VW+ Sbjct: 378 QLADGYYVEPTVF-EGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAGVWS 436 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RD +R +R R ++AG V+ N Y+ FGGYKQSG GR+ L+ + + K + + Sbjct: 437 RDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTKNMLV 496 Query: 492 S 492 S Sbjct: 497 S 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: 572 Number of extensions: 20 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: 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 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