Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 333 bits (855), Expect = 7e-96 Identities = 194/485 (40%), Positives = 290/485 (59%), Gaps = 22/485 (4%) Query: 11 FIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAAS 70 FI G++ P+ + I+P + + D++LA+DAA +A WS S Sbjct: 25 FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPA-----WSRTS 79 Query: 71 GSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEAL-ADLDDVVACFEYYAGLAEELD 129 + R+ L IA +I+ K + L +E+ID GKP+ E + ADL VV F Y+AG+ + Sbjct: 80 ATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGV---IR 136 Query: 130 SKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189 +++ + L T S +KEPIG+V I PWN+P LMATWK+APALAAGC I+KP+E Sbjct: 137 AEEGSIAELDQHTV-SVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQ 195 Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249 + + L E+ ++ LP GVLN+V G G EAG LA P +DK++FTG + TG IM Sbjct: 196 TPASIMILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQY 254 Query: 250 AAQLVKPVSLELGGKSPIVVF------EDVDLDKVAEWTVFGCFFTNGQICSATSRLIVH 303 A++ + PV++ELGGKSP V F +D LDK E V G++C+ SR++VH Sbjct: 255 ASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFAL-NQGEVCTCPSRILVH 313 Query: 304 ESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGG 363 E I F++K++ AE I++ PL++ +G S+ Q++K+L+ I K EGA +LTGG Sbjct: 314 EKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGG 373 Query: 364 ---RRPEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYG 420 + L+ GY+V+PT++ M++++EE+FGPV +V TF EEAI+++NDT YG Sbjct: 374 EVAKLNSGLENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYG 432 Query: 421 LGSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYL 480 LG+ V + D ++ +A++AG VW+NC AP+GG K+SGFGRE L +Y Sbjct: 433 LGAGVWTRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYR 492 Query: 481 SVKQV 485 K + Sbjct: 493 QNKNM 497 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: 599 Number of extensions: 21 Number of successful extensions: 7 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: 509 Length adjustment: 34 Effective length of query: 469 Effective length of database: 475 Effective search space: 222775 Effective search space used: 222775 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 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