Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 280 bits (716), Expect = 8e-80 Identities = 179/475 (37%), Positives = 265/475 (55%), Gaps = 19/475 (4%) Query: 23 YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTK 82 YI GE+ ++ G + I+P + +I ADA +AV A+A F+S +SR + + Sbjct: 8 YIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDS--FSRTSVDE 65 Query: 83 RKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDKIYDEV 142 R + + K A +LA +MG PIS + AQ S G + I Sbjct: 66 RIALLEAILAEYKNRAGDLADAIAAEMGAPIS------LAKTAQVGSGIGHLMSTINALK 119 Query: 143 AATPHDQLG--LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTA 200 A +Q+G LV EP+GVV I PWN+PL K+ PAL+ GN+++LKPSE++P +A Sbjct: 120 AFEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSA 179 Query: 201 IRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESN 260 AE+ +AG+P GV N++ G G VG AL+ H DVD + FTGST+ Q+ + E+ Sbjct: 180 AIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAET- 238 Query: 261 MKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLP 320 +KRV E GGKSPN++ A +L A + ++ N G+ C A +R+LV S + Sbjct: 239 VKRVHQELGGKSPNVILPGA-DLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQ 297 Query: 321 LVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGK-RTLQETG 379 + +KA + G+P ++G +V+ Q + I G +GA+L GG R Sbjct: 298 IASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIET 357 Query: 380 GTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADIS 439 G +V+PT+F GV N M IA+EEIFGPV+++I + EEA+ IANDT YGL+A ++ + Sbjct: 358 GYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSP-E 416 Query: 440 KAHLTARALRAGSVWVNQYDGG--DMTAPFGGFKQSGNGRDKSLHAFDKYTELKA 492 + A LRAG V++N GG D + PFGG+KQSGNGR+ ++ E+KA Sbjct: 417 EVKRVAPRLRAGMVYIN---GGQPDPSLPFGGYKQSGNGREHGKFGLAEFMEVKA 468 Lambda K H 0.316 0.132 0.390 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: 613 Number of extensions: 33 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: 497 Length of database: 474 Length adjustment: 34 Effective length of query: 463 Effective length of database: 440 Effective search space: 203720 Effective search space used: 203720 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