Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__WCS417:GFF3484 Length = 486 Score = 352 bits (902), Expect = e-101 Identities = 187/466 (40%), Positives = 279/466 (59%), Gaps = 19/466 (4%) Query: 27 NINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARYLRAIAAKIK 86 N NP+T IG++ + E+V LAV AAK A + W+ RAR +R + I+ Sbjct: 19 NYNPATGEAIGEVASGGAEEVALAVAAAKEAFPK-----WANTPAKERARLMRKLGELIE 73 Query: 87 EKKDELGKLESIDCGKPLEEALADLDDVVAC-FEYYAGLAEELDSKQKAPISLPMDT-FK 144 + L +LE++D G P+ + L + F+++A + +D S P+D Sbjct: 74 QNVPHLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGH-----SYPVDDQML 128 Query: 145 SYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVTCLELGEICKEV 204 +Y L +P+GV L++PWN PF+ ATWK AP LA G A+LK SEL+ +T ELG + E Sbjct: 129 NYTLYQPVGVCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEA 188 Query: 205 GLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQLVKPVSLELGGK 264 G+P GVLN++ G G AG +L HPDV ISFTG +ATG KIM TA +K S+ELGGK Sbjct: 189 GIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG--LKKYSMELGGK 246 Query: 265 SPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDKLVKWAENIKIS 324 SP+++FED DL++ + +F F NG+ C+A SR+ + ES+ +FV + A+ + + Sbjct: 247 SPVLIFEDADLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIVG 306 Query: 325 DPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGG-----RRPEHLKKGYFVEPTI 379 DP + ++G ++++A Y KV I EGAT+L GG P HL KG F++PT+ Sbjct: 307 DPQDPKTQVGSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAHLSKGQFIQPTV 366 Query: 380 ITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERCERLSKA 439 DV M+I +EE+FGPV+ + F E EA+ LANDT YGL S + + D+ + RL++ Sbjct: 367 FADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDIGKAHRLARG 426 Query: 440 LQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485 ++AG+V+IN ++ P+GG+K SG GRE G++ E + +K V Sbjct: 427 IEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNV 472 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: 587 Number of extensions: 19 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: 486 Length adjustment: 34 Effective length of query: 469 Effective length of database: 452 Effective search space: 211988 Effective search space used: 211988 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