Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 309 bits (791), Expect = 3e-88 Identities = 181/467 (38%), Positives = 255/467 (54%), Gaps = 23/467 (4%) Query: 13 FIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSRV 72 FI G F + +P+ G +V + +IEAAV AAR A P+W+ Q +RV Sbjct: 36 FIGGTFQAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWARV 95 Query: 73 LNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQMD 132 L +A LL++ FA E+ D GK + +R +DIP + ++F + A + E Sbjct: 96 LYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDELPD-- 153 Query: 133 HLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLCK 192 R PVGV G I PWN PL +L WKIAPA+A GNTV+ KP+E T +TA + + Sbjct: 154 ---------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLFAE 204 Query: 193 LLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSL 252 + +AGVPPGVVNIV G G G ALVSHP V I+FTGS I + +A K L+L Sbjct: 205 ICGEAGVPPGVVNIVTGDGA-TGAALVSHPGVDKIAFTGSTDVGREIRRATAGTGKALTL 263 Query: 253 ELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEATR 312 ELGGK+P ++FEDA+LD + V + + NQG++C SR+ VQ+ I F + Sbjct: 264 ELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKLRARMA 323 Query: 313 KWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQAGYF 372 ++G P D + +GA++ AH KV V + GE ++PA G F Sbjct: 324 TLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGS--------NGEVHQPGTVPAE---GAF 372 Query: 373 MLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVGRVH 432 PT+IT ++ M +EIFGPV F + E +E AN +YGLAAT+WS N+ R Sbjct: 373 YPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRAL 432 Query: 433 RVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTE 479 +A KL +G+VW N + + FGG++ SG GREG + +T+ Sbjct: 433 DIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTK 479 Score = 72.4 bits (176), Expect = 5e-17 Identities = 64/222 (28%), Positives = 103/222 (46%), Gaps = 5/222 (2%) Query: 13 FIDGKFL-PCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71 +I GK P S Y G + P + +I AV+AA A SW + R++ Sbjct: 511 YIGGKQARPDSGYSRPVWSPKGVLLGHAPEGSRKDIRNAVEAATGA-ASWGRTTGHLRAQ 569 Query: 72 VLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQM 131 +L VA+ L EEFA ++ G + A ++ ++ +A+ + + + Sbjct: 570 ILYYVAENLSARTEEFATRIAEMTGSRVPRAEA-EVSAAIDRLFTYAAWADKYDGAVKPV 628 Query: 132 DHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLC 191 G + + PVGV G +P + PL + A+A GN ++ PSE + A L Sbjct: 629 PIRG-VALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLY 687 Query: 192 KLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLI-SFTGS 232 ++LD + VP GVVNIV G + + L SH V + SF+G+ Sbjct: 688 QVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGA 729 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: 909 Number of extensions: 41 Number of successful extensions: 6 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: 780 Length adjustment: 37 Effective length of query: 450 Effective length of database: 743 Effective search space: 334350 Effective search space used: 334350 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: 53 (25.0 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