Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__HerbieS:HSERO_RS19755 Length = 484 Score = 334 bits (856), Expect = 5e-96 Identities = 190/465 (40%), Positives = 265/465 (56%), Gaps = 11/465 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKG-AWGRMSLAQRVEVLYAVADGINRRFDD 82 +P+N + A + A+V AVAAA+A L+G AW ++S QR ++L+ +A + R D Sbjct: 26 NPINEEIYASAAQGTAADVARAVAAAKAQLEGGAWSKLSGLQRGQLLHKLAALVERDTDL 85 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVG--AINYAV 140 + G+ R +D+P ++ + A + E +PT +G ++Y V Sbjct: 86 LADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQM--EGRTIPTAGYMGKPTLSYTV 143 Query: 141 RRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPP 200 R P+GVVG I PWN PL++ +WKV LA G TVV+KP+EETPQ+A L + AG P Sbjct: 144 REPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEETPQSALHLARLAQEAGFPD 203 Query: 201 GVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAA 260 GV NVV G+G NS G L HPDV I+FTG G AI + A + + V+LELGGK+ Sbjct: 204 GVINVVTGYG-NSVGRALCEHPDVAKISFTGSPEAGRAIQRIAGEQFKRVTLELGGKSPQ 262 Query: 261 IVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320 IVF D + A+ G F N GQVC R+ V+R + RF L + A G+ +G P Sbjct: 263 IVFDDAPFEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQRFAKALAEAAAGITVGDPS 322 Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380 MGP+ + E+V Y ++ ++ GAT++ GG P+ G +VQPTI+ Sbjct: 323 QPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGG--VSRPDK---GWFVQPTIFADAN 377 Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440 + +AREEIFGP ++ FD+EEE I AND+ YGLA +WTTNL+RAHRVA ++VG Sbjct: 378 NGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTTNLARAHRVAAGVKVGA 437 Query: 441 AWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 VN W D +GG K SG+GREGG+ YTE K V + L Sbjct: 438 VGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTVTVLL 482 Lambda K H 0.318 0.135 0.406 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: 566 Number of extensions: 21 Number of successful extensions: 3 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: 485 Length of database: 484 Length adjustment: 34 Effective length of query: 451 Effective length of database: 450 Effective search space: 202950 Effective search space used: 202950 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: 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