Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__Cola:Echvi_1497 Length = 469 Score = 174 bits (440), Expect = 8e-48 Identities = 127/422 (30%), Positives = 204/422 (48%), Gaps = 13/422 (3%) Query: 72 SLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSK 131 S R + L + IK + E+ K D KP E +A + E A L + Sbjct: 22 SSRIKKLEQLKEWIKSNQKEIEKALYADLRKPAAE-VAVTETSFVVMEINAALKQLPKWT 80 Query: 132 QKAPISLPMDTF--KSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189 + P+ ++Y+ EP G V +I+PWNYPF ++ + A+AAGC+A LKPSE Sbjct: 81 APTKVGQPIHMLGTQAYLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEH 140 Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249 + T L + E+ V I G G + L P D I FTGS+ G +M Sbjct: 141 SPHTSALLRRMVTELFAVEDV-TIFEG-GVPVTSELLEQP-FDHIFFTGSTEVGKIVMKA 197 Query: 250 AAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVE 309 AA+ + V+LELGGKSP ++ + DL+ A+ G F +GQ C A L VHES + Sbjct: 198 AAKNLTSVTLELGGKSPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQD 257 Query: 310 FVDKLVKWAENIKISD--PLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPE 367 F++ L + ++ + G I+ ++ N + A+++GA + GG+ Sbjct: 258 FIETLKAQVNRMYNANGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGKNSL 317 Query: 368 HLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMS 427 + F+EPT++++V+ +M + +EE+FGP+L + T+ ++ I L L + Sbjct: 318 DQQ---FMEPTVVSNVSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFT 374 Query: 428 NDLERCERLSKALQAGIVWINCAQPSFI--QAPWGGIKRSGFGRELGEWGLENYLSVKQV 485 D E+LSK +G + IN F+ + P+GGI SG GR G G + + K + Sbjct: 375 TDDRIIEQLSKNTSSGALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFSNEKAI 434 Query: 486 TR 487 + Sbjct: 435 LK 436 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: 454 Number of extensions: 22 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: 469 Length adjustment: 34 Effective length of query: 469 Effective length of database: 435 Effective search space: 204015 Effective search space used: 204015 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