Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 339 bits (869), Expect = 2e-97 Identities = 183/491 (37%), Positives = 285/491 (58%), Gaps = 17/491 (3%) Query: 4 YRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTV 61 Y N+I G++V FD ++PVDG V +V ++ A+ A H A AW RT+ Sbjct: 22 YDNFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFP-AWSRTSA 80 Query: 62 AERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPL 121 ER+ IL +IAD I+ + + A E D GKPV D+ +FR FA +++ Sbjct: 81 TERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEG 140 Query: 122 DTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEET 181 + D ++ V++P+G+VG I PWN P+L+ TWK+APALA G + KP+E+T Sbjct: 141 SIAELD----QHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQT 196 Query: 182 PGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRA 241 P + +L EV+ + +P GV N+V+GFGP+ AG+ + + +D + FTGE+ TG IM+ Sbjct: 197 PASIMILMEVIGDL-LPAGVLNVVNGFGPE-AGKPLAQSPRLDKVAFTGETTTGRLIMQY 254 Query: 242 AATHVKPVSFELGGKNAAIIF-----ADCDF-EKMIDGMMRAVFLHSGQVCLCAERVYVE 295 A+ ++ PV+ ELGGK+ + F AD +F +K ++G + L+ G+VC C R+ V Sbjct: 255 ASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFA-LNQGEVCTCPSRILVH 313 Query: 296 RPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGG 355 IY+ F++ + R +A+++G P D TT MG S + +K+LSY + ++EGA+VL GG Sbjct: 314 EKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGG 373 Query: 356 GVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYG 415 V K + G++V+PT++ G R +EE+FGP+C V+ F EAI+++NDT YG Sbjct: 374 EVAKLNSGLENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYG 432 Query: 416 LSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475 L A WT + + ++V A++ G WVN + PFGG SG GRE + LN Y Sbjct: 433 LGAGVWTRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYR 492 Query: 476 ELTNVCVRIDQ 486 + N+ + D+ Sbjct: 493 QNKNMLISYDK 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: 623 Number of extensions: 28 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: 509 Length adjustment: 34 Effective length of query: 456 Effective length of database: 475 Effective search space: 216600 Effective search space used: 216600 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