Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC
Query= SwissProt::Q9KWS5 (491 letters) >FitnessBrowser__Phaeo:GFF3171 Length = 503 Score = 352 bits (903), Expect = e-101 Identities = 197/462 (42%), Positives = 274/462 (59%), Gaps = 12/462 (2%) Query: 19 FQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAAQRVDWLRRIANEMERR 78 FQ ++P+D SV+ V +DAA +A +A EW A QR L RIA +E R Sbjct: 39 FQTISPVDKSVICDVAHGTAADIDAAAQAARQAF-AEWRDLPAVQRKKILIRIAEGIEAR 97 Query: 79 QQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVDSHRLDLPDGAYALNYA 138 ++ E DTG+ + + RG NFR FAD + A D L P +N Sbjct: 98 AEEIALCECWDTGQAYKFMSKAAL-RGAENFRYFADQVVQAR-DGQHLQSPT---LMNVT 152 Query: 139 ARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTPGTATLLAEVMEAVGIP 198 R P+G VGVI+PWN P +L TWK+APALA G VV KP+E +P TA LL E+ E G+P Sbjct: 153 TRVPIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLP 212 Query: 199 PGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAAAEGVKPVSFELGGKNA 258 PGV N V+GFG + AG+ + +HP I AI F GES+TGS I + A+ +K ELGGKN Sbjct: 213 PGVLNTVNGFG-DEAGKALCEHPAIRAIAFVGESRTGSLITKQGADTLKRNHLELGGKNP 271 Query: 259 AVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRFCVALAERIKALKVDWP 318 ++F D D E+ LD ++ ++ +G+ C S R+ ++ I D F L ERI +KV P Sbjct: 272 VIVFEDADLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHP 331 Query: 319 HETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGDERDNGAWVEPTVIAGL 378 + T++GPL+S +H +KV SYF++A +EGAT AGG G+E G ++ PT+ Sbjct: 332 LDPTTEIGPLVSEEHFNKVTSYFDIATKEGATIAAGG--EPVGEE---GYFIRPTLFTDA 386 Query: 379 SDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWTTNLSRAHRVSELMRVG 438 +D R+ +EEIFGP+ PF +E+E + ANDT YGL +WT +L+RA R ++ + G Sbjct: 387 RNDMRIAQEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAG 446 Query: 439 ISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNV 480 + WVN+ +R L TPFGG SGIGR+GG S FY E ++ Sbjct: 447 MIWVNSENVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQKHI 488 Lambda K H 0.320 0.136 0.417 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: 603 Number of extensions: 28 Number of successful extensions: 6 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: 491 Length of database: 503 Length adjustment: 34 Effective length of query: 457 Effective length of database: 469 Effective search space: 214333 Effective search space used: 214333 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