Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ac3H11_4393 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::B6ECN9 (505 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4393 Length = 507 Score = 326 bits (836), Expect = 1e-93 Identities = 199/486 (40%), Positives = 273/486 (56%), Gaps = 26/486 (5%) Query: 14 FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73 FI G++ P+K +I P + ++ +T ED+++A+ AA +A D WG T A Sbjct: 23 FIGGKFVPPVKGQYFDVITPVSGKVYTRAARSTAEDIELALDAAHAAA--DSWGKTDAAT 80 Query: 74 RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEA----L 128 RA L IA ++ E LA ET+DNGK E + DI V F Y+A A L Sbjct: 81 RANILLKIANRIEENLERLAYAETVDNGKAIRETLNADIPLTVDHFRYFAGCVRAQEGAL 140 Query: 129 DSKKQTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSE 188 + + V H+ +EPLGVVG I PWN+P+LM WK+APAL AG +LKP+E Sbjct: 141 SNIDENTVAYHI--------QEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAE 192 Query: 189 LASITSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMT 248 I+ L L E+ ++ LPPG L+I+ G G EAG PL + KIAFTGS TG I Sbjct: 193 STPISILILVELIADL-LPPGVLNIVNGFGREAGMPLAQSKRIAKIAFTGSTSTGRVIAQ 251 Query: 249 AAAQLVKPVTLELGGKSPIVVFDDIHN-----LDTAVEWTLFGCFWTNGQICSATSRLII 303 AAA + P TLELGGKSP + F DI + LD A+E + F G++C+ SR II Sbjct: 252 AAANNLIPATLELGGKSPNIFFADIMDKDDAFLDKAIEGLVLFAF-NQGEVCTCPSRAII 310 Query: 304 QETIAPQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYG 363 QE+I QF+ R+L+ IK +PL+ D +G S+ Q KIL ++ K EGA +L G Sbjct: 311 QESIYDQFMERVLKRVAAIKHQNPLDTDSMMGAQASKEQLTKILSYLDLGKQEGAEVLAG 370 Query: 364 GDRPE---HLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKF 420 G + L+ GYY+QPT+ M I++EE+FGPVL V TFK E EA+ +ANDT + Sbjct: 371 GGQAHLGGDLEGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALAIANDTLY 429 Query: 421 GLGAAILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENY 480 GLGA + S++ R +A ++G VW NC +GG K SG GRE + L++Y Sbjct: 430 GLGAGVWSRNGNVAYRMGRAIKAGRVWTNCYHAYPAHAAFGGYKESGIGRETHKMMLDHY 489 Query: 481 LNIKQV 486 K + Sbjct: 490 QQTKNL 495 Lambda K H 0.318 0.136 0.421 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: 30 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: 505 Length of database: 507 Length adjustment: 34 Effective length of query: 471 Effective length of database: 473 Effective search space: 222783 Effective search space used: 222783 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: 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