Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Marino:GFF4092 Length = 486 Score = 311 bits (796), Expect = 4e-89 Identities = 187/482 (38%), Positives = 260/482 (53%), Gaps = 13/482 (2%) Query: 4 KLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF-AEWGQTTPK 61 K ING+ V S G NPA G V+ ++ EA E+VDAAV+AA AA WG+ T + Sbjct: 5 KHYINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALRGPWGKMTLE 64 Query: 62 VRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGL 121 R L K+AD I F E E + GKP A + +IP F+ FA + + Sbjct: 65 QRTAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADMIKNVPTE 124 Query: 122 AAGEYLEGHTSMIR---RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITP 178 + T + R P GV+ I+PWN PL++ WK+ PALA GN VV+KPSE TP Sbjct: 125 SFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETP 184 Query: 179 LTALKLAELAKDI-FPAGVINILFG-RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHT 236 T L E+ K+ P GV N++ G G + G LT HP+V + TG TGE I+ Sbjct: 185 TTTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEVIMKAA 244 Query: 237 ASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTL 296 A I+ +ELGGK +VF D D+E +EG + N GQ C R+Y ++ I+D Sbjct: 245 AKGIRDISLELGGKNAGLVFADCDMEKAIEGTMRSAFANCGQVCLGTERVYVERSIFDEF 304 Query: 297 VEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG-----E 351 V +L A LK G PDD LGPL SL H E+V ++A G V+TGG Sbjct: 305 VGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDG-ATVVTGGGVPDMP 363 Query: 352 KRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVW 411 G + PT+ G D A+V E+FGP + PFD EE+ + AN YGLAS++W Sbjct: 364 AELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIW 423 Query: 412 TKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVM 471 ++++ RAHRV+ +++ G WVN+ F+ P GG K SG G++ ++ LE YT ++++ Sbjct: 424 SENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGVGREGGVHSLEFYTEMKNIC 483 Query: 472 VK 473 VK Sbjct: 484 VK 485 Lambda K H 0.317 0.134 0.397 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: 605 Number of extensions: 31 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: 474 Length of database: 486 Length adjustment: 34 Effective length of query: 440 Effective length of database: 452 Effective search space: 198880 Effective search space used: 198880 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 (21.7 bits) S2: 51 (24.3 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