Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate RR42_RS34255 RR42_RS34255 aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Cup4G11:RR42_RS34255 Length = 506 Score = 348 bits (892), Expect = e-100 Identities = 197/497 (39%), Positives = 286/497 (57%), Gaps = 19/497 (3%) Query: 2 KQYRNYINGEWVESA--RRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59 +QY NYI G W+ A + F+ ++PV G +V ++++ VD+A+ A H A +GAWGRT Sbjct: 17 EQYENYIGGAWLAPADGQYFEAISPVTGKPFTRVPRSNQKDVDAALDAAHRA-KGAWGRT 75 Query: 60 TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119 + ERA IL RIAD I+ AE D GKP+ + D+P +FR FA ++ Sbjct: 76 STTERANILNRIADRIEANLVTLAVAETIDNGKPIRETTAADLPLAVDHFRYFAGCIRAQ 135 Query: 120 PLDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSE 179 + D A Y +PLGVVG I PWN PLL+ TWK+APALA GN VV KP+E Sbjct: 136 EGGISEIDHDTVA----YHFHEPLGVVGQIIPWNFPLLMATWKLAPALAAGNCVVLKPAE 191 Query: 180 ETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIM 239 +TP + +L E++ + +PPGV N+++GFG + AG+ + ++ I I FTGE+ TG IM Sbjct: 192 QTPASILVLMEIIGDL-LPPGVLNVINGFGLE-AGKPLASSSRISKIAFTGETTTGRLIM 249 Query: 240 RAAATHVKPVSFELGGKNAAIIFAD------CDFEKMIDGMMRAVF-LHSGQVCLCAERV 292 + A+ ++ PV+ ELGGK+ I F D F+K ++G A+F L+ G+VC C R Sbjct: 250 QYASQNLIPVTLELGGKSPNIFFEDVLSADDAYFDKALEGF--AMFALNQGEVCTCPSRA 307 Query: 293 YVERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVL 352 ++ IY RF++ ++RV A+K G P D T +G S E +K+LSY L ++EGAQ L Sbjct: 308 LIQESIYERFMERALKRVAAIKQGHPLDKATMIGAQASQEQLEKILSYIDLGKQEGAQCL 367 Query: 353 VGGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDT 412 +GG G +G++V+PT+ +G R +EE+FGP+ V+ F E EA+ +ANDT Sbjct: 368 IGGERNALGGDLASGYYVKPTVFSG-HNKMRIFQEEIFGPVVSVTTFKDEEEALEIANDT 426 Query: 413 KYGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLN 472 YGL A WT + R R+ ++ G W N + FGG SGIGRE L+ Sbjct: 427 LYGLGAGVWTRDGARAFRMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHRMMLD 486 Query: 473 FYSELTNVCVRIDQEAV 489 Y + N+ V A+ Sbjct: 487 HYQQTKNLLVSYSPNAL 503 Lambda K H 0.321 0.137 0.420 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: 612 Number of extensions: 30 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: 490 Length of database: 506 Length adjustment: 34 Effective length of query: 456 Effective length of database: 472 Effective search space: 215232 Effective search space used: 215232 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