Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__BFirm:BPHYT_RS23175 Length = 497 Score = 327 bits (839), Expect = 4e-94 Identities = 190/466 (40%), Positives = 267/466 (57%), Gaps = 14/466 (3%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAAL-KGAWGRMSLAQRVEVLYAVADGINRRFDD 82 SP++ ++AKV ++G A+VDAAVAAA+ A G W ++ QR VL A I D+ Sbjct: 41 SPIDGKLLAKVADSGAADVDAAVAAARRAFDSGVWSGLNPRQRKAVLLRWAASIREHMDE 100 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142 E D GKP++ VD+P A + FA+ + + E P + R Sbjct: 101 LALLETLDAGKPIADTTSVDVPGAAYCVEWFAEAIDKIGGEV----APADHHLLGLVTRE 156 Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202 P+GVV + PWN P+L+ +WK GPALA GN+VV+KPSE++P TA L ++ AG+P GV Sbjct: 157 PIGVVAAVVPWNFPILMASWKFGPALAAGNSVVLKPSEKSPLTAIRLAQLALDAGIPAGV 216 Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMK-AAADGARPVSLELGGKNAAI 261 +NVV G G G+ L H DV+ + FTG T G+ IM+ A + V LELGGK+ I Sbjct: 217 FNVVPGAG--EPGKLLALHQDVDCLAFTGSTNVGKLIMQYAGQSNLKRVWLELGGKSPNI 274 Query: 262 VFADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320 V DC D+D+A + F N G++C R+ V R I D F+ +L A G P Sbjct: 275 VMPDCPDMDRAANAAAGAIFYNMGEMCTAGSRLLVHRDIKDVFIDKLIAAARSYTPGNPL 334 Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380 D T MG ++ + E+VL Y +A A A ++ GG + GG +++PTI+ G Sbjct: 335 DPDTSMGAIVDKVQLERVLGYI-EAGRAEAKLLLGGA---RVKEDTGGFYIEPTIFEIPG 390 Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440 + VAREEIFGP V+ FD+ EE IR AND++YGLA +WT+NL+ AH V+ + G Sbjct: 391 SGAKVAREEIFGPVLSVITFDTVEEAIRIANDSEYGLAAAVWTSNLTTAHEVSRKLRAGT 450 Query: 441 AWVNSWFL-RDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 WVN + D+ FGG KQSG GR+ +H+LE YTELK+ ++L Sbjct: 451 VWVNCYDEGGDMNFPFGGYKQSGNGRDKSLHALEKYTELKSTLVRL 496 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: 565 Number of extensions: 39 Number of successful extensions: 8 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: 497 Length adjustment: 34 Effective length of query: 451 Effective length of database: 463 Effective search space: 208813 Effective search space used: 208813 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