Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= BRENDA::B6ECN9 (505 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 326 bits (836), Expect = 1e-93 Identities = 195/482 (40%), Positives = 276/482 (57%), Gaps = 18/482 (3%) Query: 14 FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73 FI G+W P+K +I P N + +T ED+++A+ AA + D WG T+ A+ Sbjct: 22 FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIA--DKWGKTSPAE 79 Query: 74 RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132 RA L +A ++ LA ET+DNGKP E + DI V F Y+A A + Sbjct: 80 RANILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGGI 139 Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192 +++ + ++ H EPLGVVG I PWN+P+LM +WK+APAL AG +LKP+E I Sbjct: 140 -SDIDENTVAYHFH---EPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPI 195 Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252 + L L E+ ++ LPPG L+I+ G G EAG PL + + KIAFTGS TG I AAA Sbjct: 196 SILILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAAN 254 Query: 253 LVKPVTLELGGKSPIVVFDDIHN-----LDTAVEWTLFGCFWTNGQICSATSRLIIQETI 307 + P TLELGGKSP + F D+ + LD A+E + F G++C+ SR +IQE+I Sbjct: 255 SLIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSRALIQESI 313 Query: 308 APQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGGDRP 367 +F+ R L+ K IK +PL+ + +G S+ Q KIL ++ K EGA +L GG + Sbjct: 314 YDKFMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQA 373 Query: 368 ---EHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGLGA 424 L GYY+QPT+ M I++EE+FGPVL V TFK E EA+ +ANDT +GLGA Sbjct: 374 IVDGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGA 432 Query: 425 AILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLNIK 484 + S++ R +A ++G VWINC +GG K SG GRE + L++Y K Sbjct: 433 GVWSRNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTK 492 Query: 485 QV 486 + Sbjct: 493 NL 494 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: 609 Number of extensions: 29 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: 506 Length adjustment: 34 Effective length of query: 471 Effective length of database: 472 Effective search space: 222312 Effective search space used: 222312 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 Apr 09 2024. 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