Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 339 bits (870), Expect = 1e-97 Identities = 189/487 (38%), Positives = 289/487 (59%), Gaps = 16/487 (3%) Query: 15 DLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGV 74 D + + FI+G Y + +G + P G + + + A +A+ A A + Sbjct: 4 DTQPKASHFIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKAL--AAAHRAQKA 61 Query: 75 WSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEA 134 W+ ++ ++R + R A ++++ +L++LET D GKP +++ +D A AL + G Sbjct: 62 WAAMSGTERGRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGL 121 Query: 135 IDKLYDEVAATPHDQLG----LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVL 190 L E H QLG REP+GV I WN+P +ACWK PAL+ GN++V Sbjct: 122 AGSLTGE-----HIQLGEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVF 176 Query: 191 KPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAK 250 KPSE +PL AL++A + EAG+P G+ NV+ G G VG +L V + TGS K Sbjct: 177 KPSETTPLCALKVAEILHEAGLPAGIYNVVQGLGE-VGASLVTDPRVAKVSLTGSVPTGK 235 Query: 251 QLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLV 310 ++ + E MK + +E GGKSP ++F DA DL+ A A ++ G+VC+ G+R+ V Sbjct: 236 KVYAAAAEQ-MKHVTMELGGKSPLLIFDDA-DLENAVGGAILGNFYSSGQVCSNGTRVFV 293 Query: 311 ERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAG 370 ++ IK+ FL + E L G+PLD ATN G +V +QM VL YIE G ++GA+LVAG Sbjct: 294 QKGIKEAFLKRLTERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAG 353 Query: 371 GKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLA 430 G+R+ + G Y++PT+F V + M IA+EEIFGPV++V+ F+T E+AI AN T +GL+ Sbjct: 354 GRRLNRD--GFYLQPTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLS 411 Query: 431 AAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTEL 490 A V+T+D+S+AH L AGS ++N Y+ + APFGG K SG GR+ S A + Y+E+ Sbjct: 412 AGVFTRDLSRAHRVIAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEM 471 Query: 491 KSTWIKL 497 KS ++++ Sbjct: 472 KSVYVRM 478 Lambda K H 0.316 0.132 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: 583 Number of extensions: 26 Number of successful extensions: 6 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: 485 Length adjustment: 34 Effective length of query: 463 Effective length of database: 451 Effective search space: 208813 Effective search space used: 208813 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 24 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