Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_017549894.1 C792_RS0113000 aldehyde dehydrogenase family protein
Query= BRENDA::Q8VWZ1 (503 letters) >NCBI__GCF_000330705.1:WP_017549894.1 Length = 476 Score = 342 bits (876), Expect = 2e-98 Identities = 194/487 (39%), Positives = 293/487 (60%), Gaps = 20/487 (4%) Query: 6 SSRQLFIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRD 65 +S Q FIDGEW + I INP+TE+++G I T+EDV+ AV+AAK+A D Sbjct: 3 TSNQQFIDGEWVNSTSQETIEVINPATESVMGTIAKGTQEDVNKAVEAAKKAYI-----D 57 Query: 66 WSAASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLA 125 + R L I + K++K ++ + + + G P E L++ + +++ Sbjct: 58 FRQTPTKERQDMLNRIVEEYKKRKTDIIEAITEELGSPRE--LSETTHYMKGLIHFSEAR 115 Query: 126 EELDS---KQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAA 182 + LD K+K SL I+KE IGV L+TPWN+P + K+A A AAG Sbjct: 116 DALDDFAFKEKRGDSL--------IVKEGIGVTGLVTPWNFPTNQTSVKLAAAFAAGSPV 167 Query: 183 ILKPSELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSAT 242 ILKPS + L E+ + G+P+GV N+V G G G +L+SHPDV +SFTGS + Sbjct: 168 ILKPSVETPFAAIILAEVIQASGVPKGVFNLVNGRGSVIGDALSSHPDVRMMSFTGSESA 227 Query: 243 GSKIMTTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIV 302 GSKIM ++Q K VSLELGGKSP ++ +DVD+DK A+ + +GQ+C A +R ++ Sbjct: 228 GSKIMRNSSQDFKRVSLELGGKSPYIILDDVDVDKAAKSATKFVYDNSGQVCDAATRTLI 287 Query: 303 HESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTG 362 ESI EF++K + E++++ +P E+ +GP+VS Q+ V I EGAT++TG Sbjct: 288 PESIKDEFIEKAKQNMESVRVGNPNEKNMDIGPLVSRQQFNAVQGYIKKGIDEGATLITG 347 Query: 363 G-RRPEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGL 421 G +PE L++GY+V+PTI +DV M I +EE+FGPV+++ T+ST +EAI++ANDT++GL Sbjct: 348 GLGKPEGLERGYYVKPTIFSDVDNDMTIAKEEIFGPVMSIITYSTLDEAIDIANDTNFGL 407 Query: 422 GSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLS 481 VM + E ++++ AL+AG + IN P+GG K SG GRE G++G+E +L Sbjct: 408 CGYVMGENRENVQKVANALEAGSIVIN-ENAGTPDLPFGGYKHSGIGREWGDYGIEEFLE 466 Query: 482 VKQVTRY 488 VK + Y Sbjct: 467 VKALKGY 473 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: 509 Number of extensions: 18 Number of successful extensions: 4 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: 476 Length adjustment: 34 Effective length of query: 469 Effective length of database: 442 Effective search space: 207298 Effective search space used: 207298 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 24 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