Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 337 bits (863), Expect = 1e-96 Identities = 193/465 (41%), Positives = 268/465 (57%), Gaps = 21/465 (4%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 FI G F GKTF NPA +L V +G A+I+ AV AA++A W ++ Sbjct: 36 FIGGTF--QAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRA-QPAWARLGGQGW 92 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 VL + L+ + +VLE+LD GKP S IDIP A +F++ + + +E Sbjct: 93 ARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDELP 152 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 R PVGV G I PWN PLL++ WK+APALA GNTVV+KPAE TP+TA + Sbjct: 153 D----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLF 202 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253 AEIC +AGVP GVVN+V G G + GAAL HP V+ I+FTG T G+ I + A T K Sbjct: 203 AEICGEAGVPPGVVNIVTGDG--ATGAALVSHPGVDKIAFTGSTDVGREIRRATAGTGKA 260 Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313 L+ ELGGK+P V+F D++LD +E + + + NQG+VC GSR+ V+ EAF K A Sbjct: 261 LTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKLRA 320 Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLE 373 + L +GDP D VGA++ H +V ++ G + G P +G F Sbjct: 321 RMATLRIGDPLDKCIDVGAMVDPAHCAKVA---EMVAGSNGEVHQPGTVP---AEGAFYP 374 Query: 374 PTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRV 433 PT+ITGL ++++EIFGPV+ F T E +E N T YGL+A++W+ ++ RA + Sbjct: 375 PTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDI 434 Query: 434 AGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 A ++ AG+VWVN L D FGG+++SG GREGG Y++ Sbjct: 435 APKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTK 479 Score = 78.2 bits (191), Expect = 1e-18 Identities = 74/223 (33%), Positives = 100/223 (44%), Gaps = 20/223 (8%) Query: 39 LGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLD 98 LG EG +I AV+AA A + W + T + R +L V + + R EE + + Sbjct: 535 LGHAPEGSRKDIRNAVEAATGAAS--WGRTTGHLRAQILYYVAENLSARTEEFATRIAEM 592 Query: 99 TGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIR-------RPVGVI 151 TG +PRA D + T A + D IR PVGVI Sbjct: 593 TGSR--------VPRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVI 644 Query: 152 GLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNLVH 211 G P + PLL L ALA GN +V+ P+E P+ AT L ++ + VP GVVN+V Sbjct: 645 GAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVT 704 Query: 212 GFGPNSAGAALTEHPDVNAI-SFTGETTTGKIIMASAAKTLKR 253 G + L H V+A+ SF+G I A AA LKR Sbjct: 705 G-AHEALAKPLASHLGVDAVWSFSG-ADISTTIEAEAAGNLKR 745 Lambda K H 0.318 0.136 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: 910 Number of extensions: 35 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: 486 Length of database: 780 Length adjustment: 37 Effective length of query: 449 Effective length of database: 743 Effective search space: 333607 Effective search space used: 333607 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 (21.7 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