Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 342 bits (876), Expect = 2e-98 Identities = 196/497 (39%), Positives = 289/497 (58%), Gaps = 19/497 (3%) Query: 2 KQYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59 ++Y N+I G++V + F++++PV G +V + E V+ A+ A HAA + +WG+T Sbjct: 17 QRYDNFIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKK-SWGKT 75 Query: 60 TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119 + ERA +L +IAD ++ + AE D GKP+ DIP +FR FA ++T Sbjct: 76 SPTERANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQ 135 Query: 120 PLDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSE 179 D A Y +PLGVVG I PWN P+L+ WK+APALA GN VV KP+E Sbjct: 136 EGSICPIDNDTYA----YHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAE 191 Query: 180 ETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIM 239 +TP + +L E++ + +PPGV N+V GFG + AG+ + +N I I FTGE+ TG IM Sbjct: 192 QTPASIMVLIELIADL-IPPGVVNIVQGFGVE-AGKPLASNKRIAKIAFTGETTTGRLIM 249 Query: 240 RAAATHVKPVSFELGGKNAAIIFADC------DFEKMIDGMMRAVF-LHSGQVCLCAERV 292 + A+ ++ PV+ ELGGK+ I FAD F+K ++G A+F L+ G+VC C RV Sbjct: 250 QYASQNLIPVTLELGGKSPNIFFADVLDKDDDFFDKALEGF--AMFALNQGEVCTCPSRV 307 Query: 293 YVERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVL 352 V+ IY RF++ ++RV A+K G P D +T +G S E +K+LSY + ++EGA+VL Sbjct: 308 LVQESIYERFIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVL 367 Query: 353 VGGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDT 412 GGG + G +G++V+PT+ G R +EE+FGP+ V+ F E EA+A+ANDT Sbjct: 368 AGGGREELGGDLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDT 426 Query: 413 KYGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLN 472 YGL A WT + R R+ ++ G W N + L FGG SGIGRE L+ Sbjct: 427 LYGLGAGLWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLD 486 Query: 473 FYSELTNVCVRIDQEAV 489 Y + N+ V +A+ Sbjct: 487 HYQQTKNLLVSYSPKAL 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: 561 Number of extensions: 30 Number of successful extensions: 7 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