Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_057507192.1 ABB28_RS02945 aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >NCBI__GCF_001431535.1:WP_057507192.1 Length = 460 Score = 173 bits (439), Expect = 1e-47 Identities = 129/412 (31%), Positives = 208/412 (50%), Gaps = 28/412 (6%) Query: 78 LAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSL-----NID-VPGAANAL-SW 130 L P +R + + R AAL+ A + LAL + GKP+ D++ ID V AA+ L ++ Sbjct: 42 LPPHERIAILRRLAALMDAKRDHLALQIAREGGKPLPDAIIETTRAIDGVHNAADELRNF 101 Query: 131 SGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVIL 190 G I ++A + TREP+G+V AI +N PL + ++ PA++ G VI+ Sbjct: 102 GGREIPM---GLSAAAVGRWAFTTREPIGIVAAISAFNHPLNLIVHQVAPAIAVGCPVII 158 Query: 191 KPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAK 250 KP+ +PL+ + + A+ EAG+P+ G+ + ALA V L F GS ++ Sbjct: 159 KPASATPLSCLDLVAMVHEAGLPEPWCQSFMPEGNDLAEALATDKRVAFLSFIGSARVGW 218 Query: 251 QLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLV 310 L S ++ R LE GG +P IV +A DL E ++ G+VC + R+ V Sbjct: 219 SL--HSKLAHGARSALEHGGVAPAIVDRNA-DLSRIIEPIVKGGYYHAGQVCVSTQRIFV 275 Query: 311 ERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAG 370 I D F ++ ++ + G+P T+VG L+ ++ + V +I+ GAKL G Sbjct: 276 HDDIADDFTEALVARVERLRTGDPTLKDTDVGPLIQPREADRVAEWIDEAVKGGAKLATG 335 Query: 371 GKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLA 430 GKR E T ++PT+ + ++ +E+FGPV++V + +EA++ AN Sbjct: 336 GKRLSETT----LQPTVLLDPASDARVTTQEVFGPVVAVYRYADLDEAISRANSLPTAFQ 391 Query: 431 AAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTA------PFGGFKQSGNG 476 A+++T DI A A L A +V +N D TA PF G ++SG G Sbjct: 392 ASIFTQDIDIALRAANRLDASAVMIN-----DATAFRTDWMPFAGRRESGYG 438 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: 493 Number of extensions: 13 Number of successful extensions: 3 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: 460 Length adjustment: 34 Effective length of query: 463 Effective length of database: 426 Effective search space: 197238 Effective search space used: 197238 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: 51 (24.3 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