Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_010531933.1 ON01_RS15200 aldehyde dehydrogenase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >NCBI__GCF_000224785.1:WP_010531933.1 Length = 480 Score = 333 bits (855), Expect = 6e-96 Identities = 187/477 (39%), Positives = 276/477 (57%), Gaps = 8/477 (1%) Query: 23 FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82 +ING++ D+ ET + +P G ++ I D +AV A+ +F S W R+ P + Sbjct: 7 YINGKWEDSHDKETINVNNPSTGEVMTTIPRGKNDDVDKAVRAAKDSFVSEEWRRVKPFE 66 Query: 83 RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEV 142 R + LK++ +ELA LET+D+GKP++ D+ A + + G A DK+ + Sbjct: 67 RGRILCEVVAQLKENRDELARLETMDVGKPLTQGY-ADIDAAIRYFEFYGGAADKVMGDT 125 Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALR 202 + V REP+GV IVPWN+P+ + + A++ GN+VV+K +E +PLTA + Sbjct: 126 IPIEDGLIDYVIREPIGVTAHIVPWNYPIQILSRSVAAAIAMGNTVVVKSAEDTPLTAAK 185 Query: 203 IAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMK 262 IA + +P+GV N + GYG+ G AL+ H ++ L FTGS + + SN+ Sbjct: 186 IAEYFDQTDLPEGVFNHVTGYGYEAGAALSSHPLINHLTFTGSVGTG-TAVANAATSNVV 244 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV 322 + LE GGKSPNIVF+D D+ A E AI N G+ C+AGSRLL+E S K TFL + Sbjct: 245 PVTLELGGKSPNIVFSDC-DVDKAVEGVVKAIIQNAGQTCSAGSRLLIEESFKQTFLDKL 303 Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEE--TGG 380 + K G +D N+G +++ +Q + +L +I +G ++ GGKR+ E Sbjct: 304 VNKFKTLSVGPAIDD-HNLGPILNQKQFDRILEFISLAEQEGT-VLTGGKRVKYEQYENA 361 Query: 381 TYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISK 440 Y+EPTI D +S K AQEEIFGPVLSV F ++AI+IAN T YGL +WTKDI+K Sbjct: 362 CYLEPTIIDNLSLNSKAAQEEIFGPVLSVFTFKNEQEAIDIANSTDYGLVTGIWTKDINK 421 Query: 441 AHLTAKALRAGSVWVNQYD-GGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTWIK 496 AHL + +G V++N Y GG + PFGG+K+SG GR+K A YT++K+ IK Sbjct: 422 AHLLMSRIDSGQVFINNYGAGGGIQMPFGGYKKSGFGREKGWIALYNYTQVKNVAIK 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: 582 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: 480 Length adjustment: 34 Effective length of query: 463 Effective length of database: 446 Effective search space: 206498 Effective search space used: 206498 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