Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 229 bits (585), Expect = 1e-64 Identities = 143/457 (31%), Positives = 232/457 (50%), Gaps = 13/457 (2%) Query: 28 INPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARYLRAIAAKIKE 87 INP+T II + + L DA ++A + W+ + R + + ++ Sbjct: 4 INPATAEIITSLEEDNLSTLQLKFDALQKAQPQ-----WAGKTLQERIAVITHFSDLLEV 58 Query: 88 KKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSKQKAPISLPMDTFKSYI 147 + ++L + + + GKPL+++ +++ A ++ AE+ + + + K I Sbjct: 59 EIEKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADE---VMTDEPGIKEII 115 Query: 148 LKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVTCLELGEICKEVGLP 207 EP+GVV I+ WNYP+L+ PAL +G + KPSE A++T +E+ ++ K+ G+P Sbjct: 116 KYEPLGVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVP 175 Query: 208 RGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQLVKPVSLELGGKSPI 267 V +I G E G++L + D + FTGS TG I A + P LELGGK P+ Sbjct: 176 DDVFHIAIG-AKETGSALLNM-DFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPL 233 Query: 268 VVFEDV-DLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDKLVKWAENIKISDP 326 + +DV D+ A T G F+ NGQ C A R+ V E ++ + V ++ K P Sbjct: 234 YITDDVTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIP 293 Query: 327 LEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPEHLKKGYFVEPTIITDVTTS 386 EG +G + + Q + N + A ++GA +LTGG+ E KGY+ EPT++TDVT Sbjct: 294 TAEGVYIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEG--KGYYFEPTVLTDVTND 351 Query: 387 MQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERCERLSKALQAGIVW 446 M + +EE FGP++ + + EA+ + DT YGL ++V + ER E++ L AG + Sbjct: 352 MLVMQEESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGY 411 Query: 447 INCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVK 483 NC PW G K SG G L G+ + K Sbjct: 412 WNCCDRVSAALPWSGRKYSGIGATLSHQGIRAFTKPK 448 Lambda K H 0.317 0.134 0.402 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: 468 Number of extensions: 23 Number of successful extensions: 5 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: 503 Length of database: 454 Length adjustment: 34 Effective length of query: 469 Effective length of database: 420 Effective search space: 196980 Effective search space used: 196980 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 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