Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_012708832.1 NGR_RS22740 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-13349 (490 letters) >NCBI__GCF_000018545.1:WP_012708832.1 Length = 502 Score = 341 bits (875), Expect = 3e-98 Identities = 196/496 (39%), Positives = 285/496 (57%), Gaps = 19/496 (3%) Query: 3 QYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60 +Y N+I GEW E + R FD+ PV G + Q+ +D ++ A+ A HAA + WGRT+ Sbjct: 14 KYGNFIGGEWREPVAGRYFDNTTPVTGGSLCQIARSDAADIELALDAAHAA-KEKWGRTS 72 Query: 61 VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120 ER+ IL +IA ++ + AE D GKP+ DIP +FR FA ++ Sbjct: 73 TTERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQE 132 Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180 + D A Y +PLGVVG I PWN P+L+ WK+APALA GN VV KP+E+ Sbjct: 133 GSIGEIDHDTVA----YHFHEPLGVVGQIIPWNFPILMAAWKVAPALAAGNCVVLKPAEQ 188 Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240 TP + +LAE++ + +PPGV N+V+GFG + AG+ + T+ I I FTGE+ TG IM+ Sbjct: 189 TPASILILAELIADL-LPPGVLNIVNGFGLE-AGKPLATSPRIAKIAFTGETTTGRLIMQ 246 Query: 241 AAATHVKPVSFELGGKNAAIIFADC------DFEKMIDGMMRAVF-LHSGQVCLCAERVY 293 A+ ++ PV+ ELGGK+ I FAD F+K ++G A+F L+ G+VC C R Sbjct: 247 YASQNLIPVTLELGGKSPNIFFADVLNEDDDYFDKALEGF--AMFALNQGEVCTCPSRAL 304 Query: 294 VERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLV 353 V+ IY+RF++ V+RV+A++ G P D T +G S E +K+LSY + ++EGA+VL Sbjct: 305 VQESIYDRFMERAVKRVEAIRQGNPLDSATMIGAQASGEQLEKILSYIDIGKQEGAEVLA 364 Query: 354 GGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTK 413 GGG G++V+PT+ G R +EE+FGP+ V+ F TE EA+ +ANDT Sbjct: 365 GGGRNVLEGDLAGGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEDEALEIANDTL 423 Query: 414 YGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNF 473 YGL A W+ + NR +R ++ G W N + FGG SGIGRE L+ Sbjct: 424 YGLGAGVWSRDANRCYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDH 483 Query: 474 YSELTNVCVRIDQEAV 489 Y + N+ V +A+ Sbjct: 484 YQQTKNMLVSYSPKAL 499 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: 580 Number of extensions: 32 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: 502 Length adjustment: 34 Effective length of query: 456 Effective length of database: 468 Effective search space: 213408 Effective search space used: 213408 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 Apr 09 2024. 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