Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein
Query= SwissProt::Q9H2A2 (487 letters) >NCBI__GCF_000015565.1:WP_011810430.1 Length = 798 Score = 311 bits (798), Expect = 4e-89 Identities = 177/463 (38%), Positives = 262/463 (56%), Gaps = 21/463 (4%) Query: 12 NFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQER 69 +FI G+F+ + Y + ++P+T E RV + +I+ AV AAR+A P+WS S +R Sbjct: 36 HFIHGEFVAPAQNEYFEVFNPATEERLARVAHGSDADIDQAVAAARQALPAWSGLSGHQR 95 Query: 70 SRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECT 129 +R L +A L++ FA E+ D GKT+ +R +DIP V++F HH Sbjct: 96 ARYLYAIARHLQKHARFFAVLETMDNGKTIRESRDIDIPLVVRHF-------YHHAGWAQ 148 Query: 130 QMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWM 189 +D + VGV G I PWN PL +L WK+APA+AAGNTV+ KP+E T +TA Sbjct: 149 LLDS----EFPAHQAVGVCGQIVPWNFPLLMLAWKVAPALAAGNTVVLKPAEFTPLTALA 204 Query: 190 LCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKK 249 +L + G+P GV+NIV G G G +LV+H V I+FTGS I + +A KK Sbjct: 205 FAELCVEVGLPAGVLNIVTGDG-HTGASLVNHAGVDKIAFTGSTAVGRLIRRATAGTDKK 263 Query: 250 LSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVE 309 LSLELGGK+P I+F+DA+LD + V S + NQG++C SRI VQ+S+ + F + Sbjct: 264 LSLELGGKSPFIVFDDADLDAAVEGVVDSIWFNQGQVCCAGSRILVQESVAARFGDKLRA 323 Query: 310 ATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQA 369 RK ++G P D +GA++ + L+++R V+ A+G W L P+ + Sbjct: 324 RMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRADGLSCW----QTALDAPS---S 376 Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429 G+F PT D+ EEIFGPV + F + +E + AN+ +YGLAA++WS N+ Sbjct: 377 GHFFAPTFFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANHSRYGLAASLWSENID 436 Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKD 472 VA +L +G+VW N + + FGG + SG GREG ++ Sbjct: 437 VCLTVAAQLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGRE 479 Score = 74.3 bits (181), Expect = 1e-17 Identities = 68/245 (27%), Positives = 105/245 (42%), Gaps = 20/245 (8%) Query: 13 FIDGKFL-PCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71 +I GK + P S Y +G + + +I AV+ AR+A +WS S R++ Sbjct: 527 YIGGKQVRPDSGYSFGVRSGSGALLGHAGFGNRKDIRNAVETARKA-GNWSQASGHARAQ 585 Query: 72 VLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQM 131 VL A+ L + F G + A A Q F + H+ + + Sbjct: 586 VLYYFAENLGARAQTFIAHLQAIDGISEAAAS--------QQFEQVLARVFHYAAMADKH 637 Query: 132 DHLGCMHYTVRA--------PVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELT 183 D G +H T+ A P GV G+ SP + PL P +A GN V+ P Sbjct: 638 D--GSVHSTLTAHVTLAMNEPFGVVGVRSPAHTPLLAALSLALPLLATGNRVVLVPPPDA 695 Query: 184 SVTAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLS 243 S+ L ++LD + +P GV+NIV+G + E L H +V + + G A R+ S Sbjct: 696 SLMFADLYQVLDTSDMPAGVLNIVWGDSDELAEVLALHDDVDALWYFGPAAGAARVQAAS 755 Query: 244 APHCK 248 A + K Sbjct: 756 AGNLK 760 Lambda K H 0.319 0.133 0.404 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: 914 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 487 Length of database: 798 Length adjustment: 37 Effective length of query: 450 Effective length of database: 761 Effective search space: 342450 Effective search space used: 342450 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: 54 (25.4 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