Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate SMa1731 SMa1731 betaine aldehyde dehydrogenase
Query= SwissProt::Q9KWS5 (491 letters) >FitnessBrowser__Smeli:SMa1731 Length = 489 Score = 332 bits (851), Expect = 2e-95 Identities = 187/479 (39%), Positives = 272/479 (56%), Gaps = 15/479 (3%) Query: 6 NFVDGKWVE--SSKTFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAAQ 63 +F+DG ++E + V P+DG ++A +H A +++ A+ + RA + EW R A+ Sbjct: 20 HFIDGTFIEDRTGPEILSVNPVDGEIIAKLHGATSCIIEKAIASAKRA-QKEWARKEPAE 78 Query: 64 RVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVDS 123 R L R A+ M R ++ E DTGKP+S D G F I AT DS Sbjct: 79 RGRVLSRAADIMRARNRELSVLETRDTGKPISETLVADAASGADCLEYFGAIAATLSGDS 138 Query: 124 HRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTPG 183 + D Y R+PLGV I WN P+ + WK APALACGNA++ KPSE TP Sbjct: 139 IQFG-EDWVYT----RREPLGVCLGIGAWNYPIQIAAWKAAPALACGNAMIFKPSEVTPL 193 Query: 184 TATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAAA 243 +A LAE++ G+PPGVFN+V G G G ++ HP I+ ++ TG KTG+ + AA Sbjct: 194 SALKLAEILTEAGLPPGVFNIVQGAG--DVGAELATHPAIAKVSLTGSVKTGARVASAAM 251 Query: 244 EGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRFC 303 G++PV+ ELGGK+A ++F D D E + G + F ++GQ+C RV+++R I + F Sbjct: 252 AGIRPVTMELGGKSALIVFDDADVEAAVSGAILGNFYSAGQICSNGTRVFLQRGIREAFL 311 Query: 304 VALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGDE 363 L R+ ALK+ P + +T +GPL+S+ HR++V +Y A EGA +A GD Sbjct: 312 ARLLARVAALKIGDPMDEETDIGPLVSAAHRNRVATYVARAEVEGAYQMAPPRKLPPGD- 370 Query: 364 RDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWTT 423 AW EP V ++D + REE+FGP+ V FD E +V+ RAN T +GLAA I+T Sbjct: 371 ----AWHEPVVFTNVTDWMTLAREEVFGPVMAVLDFDDEQDVVARANATDFGLAAGIFTR 426 Query: 424 NLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNVCV 482 +L RAHR++ + G W+N + L FGG SGIGRE G +++ Y++L +V V Sbjct: 427 DLVRAHRLAAELEAGTVWINAYNLTPAGMAFGGIKRSGIGRENGRVAIDHYTQLKSVFV 485 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: 605 Number of extensions: 28 Number of successful extensions: 5 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 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