Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::B6ECN9 (505 letters) >FitnessBrowser__Marino:GFF3202 Length = 533 Score = 337 bits (865), Expect = 5e-97 Identities = 196/496 (39%), Positives = 287/496 (57%), Gaps = 21/496 (4%) Query: 14 FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73 +I GEW P+K I P +I IP ++ ED+D+A+ AA A WG T+ + Sbjct: 49 YIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPA--WGKTSPTE 106 Query: 74 RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132 R+ L IA ++ +LA ET DNGK E + DI F Y+A A + Sbjct: 107 RSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGH- 165 Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192 E+ + ++ H EPLGVVG I PWN+P+LM WK+ P LAAG +LKP+E Sbjct: 166 MGEIDHNTVAYHFH---EPLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPA 222 Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252 + L L EI ++ LPPG L+I+ G G EAG L + + KIAFTGS P G I+ AA+ Sbjct: 223 SILVLMEIIGDL-LPPGVLNIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAE 281 Query: 253 LVKPVTLELGGKSPIVVFDDIHN-----LDTAVEWTLFGCFWTNGQICSATSRLIIQETI 307 + P T+ELGGKSP + F D+ +D VE + F+ G++C+ SR ++QE + Sbjct: 282 NIIPSTVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLA-FFNQGEVCTCPSRALVQEDM 340 Query: 308 APQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGGDRP 367 +F+ ++++ TK+IK +PL+ D ++G S+ Q++KI+ +++ K+EGA +L GGDR Sbjct: 341 FEEFMQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDRE 400 Query: 368 ---EHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGLGA 424 E G+YIQPT+ D M +++EE+FGPV+ V TFKTEEEA+ +ANDT+FGLGA Sbjct: 401 HLDEEFNNGFYIQPTLFKG-DNKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGA 459 Query: 425 AILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLNIK 484 + ++D R + Q+G VW+NC +GG K+SG GRE + +LE+Y K Sbjct: 460 GVWTRDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTK 519 Query: 485 -QVTQYVTPDEPWAFY 499 +T Y T P F+ Sbjct: 520 CMLTSYDT--NPLGFF 533 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: 662 Number of extensions: 26 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: 533 Length adjustment: 35 Effective length of query: 470 Effective length of database: 498 Effective search space: 234060 Effective search space used: 234060 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