Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate WP_086509897.1 BZY95_RS10630 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9KWS5 (491 letters) >NCBI__GCF_002151265.1:WP_086509897.1 Length = 489 Score = 347 bits (891), Expect = e-100 Identities = 192/481 (39%), Positives = 274/481 (56%), Gaps = 11/481 (2%) Query: 7 FVDGKW--VESSKTFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAAQR 64 ++DG+ S +TF + P DGS++A V +A + +D AV + + + W T QR Sbjct: 10 YIDGRREPATSGETFDVLNPYDGSLLARVDQASQADIDRAVASASQG-QRRWAAMTGMQR 68 Query: 65 VDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVDSH 124 L+R + R + + E +TGKP+S A +DI G +A + ++ Sbjct: 69 GRVLQRAVALLRERNDELAELETRNTGKPISETAAVDIVTGADVLEYYAGLAPA--IEGA 126 Query: 125 RLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTPGT 184 ++ L + ++ Y R+PLGV+ I WN P+ + WK APALA GNAVV KPSE TP T Sbjct: 127 QIPLRESSFV--YTRREPLGVIAAIGAWNYPIQIACWKAAPALAAGNAVVFKPSEVTPLT 184 Query: 185 ATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAAAE 244 A LAE+ VG+P GVFN+VHG G+ ++ H I+ ++FTGE TG +M AA Sbjct: 185 AMKLAEIFTEVGLPDGVFNVVHGEA--RVGQMLTAHEGIAKVSFTGEVGTGKKVMAAAGG 242 Query: 245 G-VKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRFC 303 +K V+ ELGGK+ ++FAD D ++ D M A F +SGQ+C RV+VER + F Sbjct: 243 STLKDVTMELGGKSPLIVFADADLDRAADAAMMANFYSSGQICTNGTRVFVERSVKAAFE 302 Query: 304 VALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGDE 363 + ER+ ++ P + + GPL+S +H+ KVL Y +Q+GA L GG GD Sbjct: 303 EKIVERVARIRAGDPLDPEINFGPLVSFEHQAKVLDYIAYGKQDGARVLIGGEPLDEGDF 362 Query: 364 RDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWTT 423 GAW TV SD+ R+VREEIFGP+ + FD E E+IRRANDT YGLAA ++T Sbjct: 363 A-RGAWAPATVFTDCSDEMRIVREEIFGPVMSILVFDDEEELIRRANDTHYGLAAGVFTE 421 Query: 424 NLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNVCVR 483 +L+RAHR M GI W+NTW P GG SG+GRE G+ +L Y++ +V V Sbjct: 422 SLARAHRTIHRMEAGICWINTWGESPAEMPVGGYKQSGVGRENGIETLAHYTQTKSVQVE 481 Query: 484 I 484 + Sbjct: 482 M 482 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: 635 Number of extensions: 32 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: 489 Length adjustment: 34 Effective length of query: 457 Effective length of database: 455 Effective search space: 207935 Effective search space used: 207935 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 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