Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf6N2E2_4679 Betaine aldehyde dehydrogenase (EC 1.2.1.8)
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4679 Length = 490 Score = 351 bits (901), Expect = e-101 Identities = 189/479 (39%), Positives = 277/479 (57%), Gaps = 5/479 (1%) Query: 21 RAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAP 80 + YI+G Y+ A TFE I+P +G +LA V D +RAV +A VW+ + Sbjct: 8 KLYIDGAYSDASGDATFEAINPANGEVLAQVQRATFEDVERAVVSAEK--GQKVWAAMTA 65 Query: 81 AKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYD 140 +R + R +L+ +ELA LETLD GK S++ +D+ + L + + I Sbjct: 66 MQRSRILRRAVDILRERNDELAALETLDTGKAYSETRYVDIVTGTDVLEYYAGLVPAIEG 125 Query: 141 EVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTA 200 E REP+GVV I WN+P+ +A WK PAL+ GN++I KPSE + LT Sbjct: 126 EQIPLRDTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTT 185 Query: 201 IRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESN 260 +++A + EAG+P GVFNVL G G VG L H ++ + FTG T K+++ + S+ Sbjct: 186 LKLAEIYTEAGVPPGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSS 245 Query: 261 MKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLP 320 +K V +E GGKSP I+F DA DL AA++A A ++ G+VCT G+R+ V +K F Sbjct: 246 LKDVTMELGGKSPLIIFDDA-DLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEA 304 Query: 321 LVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTL--EET 378 + E + + GNP D TN G LV M +VL YIE G A+GA+L+ GG R E Sbjct: 305 KIAERVARIRIGNPEDENTNFGPLVSFAHMESVLGYIEKGKAEGARLLCGGNRLTDGELA 364 Query: 379 GGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADI 438 G +V PT+F T+ M I +EEIFGPV+S++T+++ EE + ANDT +GLAA V T D+ Sbjct: 365 KGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGVVTRDL 424 Query: 439 SKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIKL 497 ++AH L AG W+N + D P GG+KQSG GR+ + + + +T +K+ ++L Sbjct: 425 NRAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483 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: 608 Number of extensions: 32 Number of successful extensions: 4 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: 490 Length adjustment: 34 Effective length of query: 463 Effective length of database: 456 Effective search space: 211128 Effective search space used: 211128 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