Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate H281DRAFT_03644 H281DRAFT_03644 betaine-aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_03644 Length = 499 Score = 331 bits (848), Expect = 4e-95 Identities = 184/496 (37%), Positives = 281/496 (56%), Gaps = 11/496 (2%) Query: 1 MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQ 60 MT +T D L G +I GE+ G+ ++ + P D + +++ +A DA+ Sbjct: 1 MTDMTHFD-----TSLVPTGDIFIGGEWRQG-RGNPYKSLYPADQSVNMEISTANADDAR 54 Query: 61 RAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNID 120 AVE A + WS L P +R + R A L+ A E LA L+ D GKPI ++ + Sbjct: 55 EAVEAADIAWRKSDWSGLKPHQRALILYRIADLIMARHEALAQLQRRDNGKPIGET-RVL 113 Query: 121 VPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180 V AAN + ++ + +EV + D L + EP+GV+ AI PWN P+ KL P Sbjct: 114 VASAANTFRYFAACLETLDEEVTPSRGDYLTMSVYEPIGVIAAITPWNSPIASDAQKLAP 173 Query: 181 ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTL 240 AL+ GN+V+LKP+E +PL ++ +A + EAG+PKGV +VLPG G +G+ L H V + Sbjct: 174 ALAGGNAVVLKPAEVTPLVSLALARICEEAGVPKGVISVLPGKGSVIGDVLVRHPLVKKV 233 Query: 241 VFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGE 300 FTG T++ + + R + V LE GGKSP +VF DA DL A I + GE Sbjct: 234 SFTGGTEVGRG-IARIAADKLMPVSLELGGKSPTVVFDDA-DLDHAVNGVLYGIFSSSGE 291 Query: 301 VCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360 C AGSRL V+RS+ D F+ ++E + + G+P T +G L+ TV Y+ G Sbjct: 292 ACIAGSRLFVQRSVYDAFMKRLVEGARKLRVGDPSRVETQMGPLITQAHRETVERYVALG 351 Query: 361 HADGAKLVAGGKRTLEE--TGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEA 418 +G +L+ GG+R + + GTY +PTI +G++N +I +EEIFGPVL + FD Sbjct: 352 LEEGGRLLCGGERPVGDGREQGTYFQPTILEGLSNNARICQEEIFGPVLVAMPFDDEASL 411 Query: 419 VAIANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRD 478 + AN++++GLAA +WT D +A+ TA+AL AG++W+N Y ++ PF G+K+SG GR+ Sbjct: 412 LKEANNSVFGLAAGIWTRDYKRAYRTARALEAGTIWINTYKLFSISTPFSGWKESGMGRE 471 Query: 479 KSLHAFDKYTELKATW 494 K +Y + K+ + Sbjct: 472 KGRLGIREYMQQKSLY 487 Lambda K H 0.316 0.132 0.386 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: 658 Number of extensions: 26 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: 497 Length of database: 499 Length adjustment: 34 Effective length of query: 463 Effective length of database: 465 Effective search space: 215295 Effective search space used: 215295 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 (21.6 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