Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 326 bits (836), Expect = 1e-93 Identities = 197/485 (40%), Positives = 274/485 (56%), Gaps = 14/485 (2%) Query: 15 SLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGD 74 SL + N I+G A + E +P T A D+D A++AA V Sbjct: 3 SLRLAN--LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAA--VAAAPG 58 Query: 75 WSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEA 134 W+ + +R +L +LADL+EA +E A LE+ D+GKP+ + DIP A +R++A A Sbjct: 59 WAATPSEQRARLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAA 118 Query: 135 IDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSE 194 I E + +R+P+GV+A I PWN PL L WK+ PALAAGN+V+ KPSE Sbjct: 119 IVPWSSESHAMELGAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSE 178 Query: 195 KSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLK 254 +P +A L L+ EAG P GVLN+V G G E GQAL H D+ A++FTGSTRTG Q+ Sbjct: 179 ITPCTAALLGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAA 238 Query: 255 DAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASAT-AAGIFYNQGQVCIAGTRLLLEES 313 A K++ LE GGK+ IVFAD DL A T F NQG++C+ G+RLL++ S Sbjct: 239 -AAAPRFKKLSLELGGKNPAIVFADA-DLSDANLDTIVRSGFANQGEICLCGSRLLVQRS 296 Query: 314 IADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA 373 I D F + + + G P + AT +G L+ H D V I + ++G +L G +A Sbjct: 297 IYDAFRERYLAKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDA 356 Query: 374 ----GLAAA---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLG 426 G A + PT+ + P + +++EIFGPV+ + F E QAL +AN + YGL Sbjct: 357 LALPGPLAGGWYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLA 416 Query: 427 AAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTEL 486 A++WT DLSRAHR +L G V++N + D+ PFGG KQSG GR+ + AL FTE Sbjct: 417 ASLWTTDLSRAHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEP 476 Query: 487 KTIWI 491 K I I Sbjct: 477 KNICI 481 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: 549 Number of extensions: 23 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: 483 Length adjustment: 34 Effective length of query: 461 Effective length of database: 449 Effective search space: 206989 Effective search space used: 206989 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