Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate SM_b21301 SM_b21301 ly membrane-anchored aldehyde dehydrogenase
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__Smeli:SM_b21301 Length = 794 Score = 330 bits (847), Expect = 8e-95 Identities = 192/467 (41%), Positives = 267/467 (57%), Gaps = 22/467 (4%) Query: 3 EIKHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLS 62 ++ HFINGAFVGSASG++F+ P+ G+++ + GR +V+AAV AAR A +GPW KLS Sbjct: 32 KLGHFINGAFVGSASGKSFDTFEPATGKLLAKIAHGGRDDVNAAVAAARKA-QGPWAKLS 90 Query: 63 VAERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVA 122 RA L+ +A I E LD GKP IDIP A +F A + Sbjct: 91 GHARARHLYALARLIQRHARLIAVVEALDNGKPIRETRDIDIPLAARHFYHHAGWAQLQE 150 Query: 123 NEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEE 182 E +A + P GV+G + PWN P L++ WKV PALA GN+V++KP+E Sbjct: 151 TE--------------FADQVPVGVVGQVIPWNFPFLMLAWKVAPALALGNSVILKPAEF 196 Query: 183 TPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMR 242 TPLTA L E+ AAG+P GV NVV G G GA + EH D+D FTG T G +I Sbjct: 197 TPLTALLFAELAAAAGLPPGVLNVVTGEG--ETGALIVEHEDIDKIAFTGSTEVGRLIRE 254 Query: 243 AAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFD 302 A + ++LELGGK+ IVF D D+D A+EG + + + N GQVC R+ V+ + Sbjct: 255 KTAGSGKSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVCCAGSRLLVQEGVAP 314 Query: 303 EFVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDM 362 F RLK E+L +G P D + + +V+ +++ + V +G S+ ++ Sbjct: 315 VFHDRLKRRMETLRVGHPLDKAIDMAAIVAPVQLQRIEELVAKGVAEGASMHQPK--IEL 372 Query: 363 PAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAI 422 P GG++ +PT+ TG+ S V TEEIFGP F T EEAI+LAN YGLA+++ Sbjct: 373 PK---GGSFFRPTLLTGVQPTSVVATEEIFGPVAVSMTFRTPEEAIQLANHSRYGLAASV 429 Query: 423 WTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGG 469 W+E A VA ++ AG+VWVN+ L D + FGG ++SG GREGG Sbjct: 430 WSETIGLALHVAAKLAAGVVWVNATNLFDASSGFGGKRESGFGREGG 476 Score = 95.9 bits (237), Expect = 5e-24 Identities = 80/255 (31%), Positives = 121/255 (47%), Gaps = 28/255 (10%) Query: 29 GQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAERAEILHRVADGITARFDEFLEAE 88 G+VIG V E R ++ AV AAR A W + RA+IL+ +A+ +++R EF Sbjct: 543 GKVIGEVGEGNRKDIRNAVVAARGA--SGWSSATAHNRAQILYYIAENLSSRGAEFAGRI 600 Query: 89 CLDTGKPKSLASHIDIPRGAA---NFKVFADLLKNVANEAFEMATPDGAGAINYAVRRPK 145 TG + A ++ A ++ +AD + ++ P G + A+ P+ Sbjct: 601 AAMTGASAANA-RAEVEASIARLFSYGAWADKYEGTVHQ------PPLRG-VALAMPEPQ 652 Query: 146 GVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPLTATLLGEVMQAAGVPAGVYN 205 GV+GVI P PLL + V P +A GN VV PSE PL AT V++ + VP GV N Sbjct: 653 GVVGVICPPEAPLLGLVSLVAPLIAVGNRVVAVPSEAHPLAATDFYSVLETSDVPPGVIN 712 Query: 206 VVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAAKGVRQVSLELGGKNAGIVFA 265 +V G + A A L H DVDA G ++ + + +++ ++ G Sbjct: 713 IVTGSAIELAKA-LAAHNDVDALWAFGSPELSTLVEKLSVGNLKRTFVDYG--------- 762 Query: 266 DCDMDKAIEGTLRSA 280 KAI+ T RSA Sbjct: 763 -----KAIDWTDRSA 772 Lambda K H 0.318 0.136 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: 1045 Number of extensions: 50 Number of successful extensions: 7 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: 794 Length adjustment: 37 Effective length of query: 449 Effective length of database: 757 Effective search space: 339893 Effective search space used: 339893 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