Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 294 bits (753), Expect = 4e-84 Identities = 177/478 (37%), Positives = 261/478 (54%), Gaps = 12/478 (2%) Query: 7 YINGEWV--ESARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTVAER 64 Y++G WV + RRFD ++P G ++A V + AI A AA W + T +R Sbjct: 28 YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN-PWRQRTAKDR 86 Query: 65 AAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPLDTF 124 AA++ D I D A+ GKP+A A +I GA+ FA+ K A D Sbjct: 87 AAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMG-EISYGASFISWFAEEGKRAYGDLI 145 Query: 125 QTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGT 184 T D R L +++P+GVV ++PWN P+ ++T K APALA G VV KP+E+TP + Sbjct: 146 PTTASD--RRL-LVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLS 202 Query: 185 ATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAAT 244 A LAE+ H G+P G+FN+V P + G +T N + ++FTG +R G +M A Sbjct: 203 ALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAE 262 Query: 245 HVKPVSFELGGKNAAIIFADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLD 304 VK VS ELGG I+F DCD + + G + + + +SGQ C+C R V+ IY F Sbjct: 263 TVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAV 322 Query: 305 AFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVPKFGDAR 364 E+ A+ +G G GPLI+A KV ++ A +GA+VL GG G Sbjct: 323 KLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRPHALG--- 379 Query: 365 DAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGN 424 GFW +PT++ + C +EE FGP+ + F+TEAEAIALAN +++GL+ ++ + Sbjct: 380 -GGFW-QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRD 437 Query: 425 LNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYSELTNVCV 482 + R RV+EA+ G+ VN + + PFGG+ SG+GREG + L+ + E VC+ Sbjct: 438 VARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYVCI 495 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: 657 Number of extensions: 41 Number of successful extensions: 3 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: 499 Length adjustment: 34 Effective length of query: 456 Effective length of database: 465 Effective search space: 212040 Effective search space used: 212040 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