Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 336 bits (862), Expect = 9e-97 Identities = 184/469 (39%), Positives = 276/469 (58%), Gaps = 8/469 (1%) Query: 24 DASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAARI 83 +++ T PA VI GE EV AV AK AF W+ +R ++L + + Sbjct: 12 ESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRAKLLRKVGDL 71 Query: 84 IREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLPGGSFGYT 142 I + DEIA +E ++ G+S + + + + + ++A + GE YT Sbjct: 72 INQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPT-NDHLNYT 130 Query: 143 RREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGVP 202 +P+GV I WN PF A+WK+AP LA GN V K S +P+SA L ++ EAG+P Sbjct: 131 LYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLGQLILEAGIP 190 Query: 203 PGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPL 261 G+FN+V G G+A G+ L +HPDV VSFTGS TG +I++ G+K ++ELGGKSP Sbjct: 191 AGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSG--GLKKYSMELGGKSPN 248 Query: 262 IIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPL 321 IIF DCD AV A++A + G+ C NGTR+ VQ + D+F + ++T+++ +GDPL Sbjct: 249 IIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERTRKVVVGDPL 308 Query: 322 LEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPED--PKLKDGYYMRPCVLT 379 E T +GP+I R H ++V ++++ +GA+V+ GG + PE P LK+G ++RP VL Sbjct: 309 DEATNVGPMITRDHWKKVTSYIELGISEGARVVAGG-LGTPEGLAPHLKNGNFVRPTVLA 367 Query: 380 NCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQ 439 + + +EEIFGPV ++ F EAE L+ AN T++GLA+ V+T + RA R+ ++ Sbjct: 368 DVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARAIRMAEGIE 427 Query: 440 AGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMG 488 AG F+N+ NV + PFGG K SG GRE G + E + ++K VCV G Sbjct: 428 AGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVSKG 476 Lambda K H 0.320 0.137 0.411 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: 599 Number of extensions: 26 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: 494 Length of database: 485 Length adjustment: 34 Effective length of query: 460 Effective length of database: 451 Effective search space: 207460 Effective search space used: 207460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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