Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 158 bits (400), Expect = 8e-43 Identities = 142/468 (30%), Positives = 209/468 (44%), Gaps = 39/468 (8%) Query: 23 NPVDGT-VVAQVHEADREAVDSAIRAGHAAVRGAWGRTTVAERAAILCRIADEIDRRYDD 81 NP D VV AD V+ A+ AA G W R A RAAIL A++++ R + Sbjct: 600 NPADRRQVVGSYVSADSATVEKALANAVAAQHG-WDRLPAASRAAILEHAAEQLEARRGE 658 Query: 82 FLAAEIADTGKPVAMASTIDIPRGAANFRVFADILK---TAPLDTF--QTDLPDGARALN 136 F+A + + GK +P A R AD L+ T F LP N Sbjct: 659 FIALCVREAGK--------GLPDAIAEIREAADFLRYYATMARRYFGQPEQLPGPTGESN 710 Query: 137 YAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGTATLLAEVMHTVG 196 GV ISPWN PL + ++A ALA GN+V+AKP+E+T +++H G Sbjct: 711 QLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHEAG 770 Query: 197 VPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAATHVKPVS---FEL 253 VP V + G G + G +T + + + FTG + T AI RA A P++ E Sbjct: 771 VPADVLQYLPGDGA-TVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAALIAET 829 Query: 254 GGKNAAIIFADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLDAFVERVKAL 313 GG+NA I + E+++ + + F +GQ C A +YV+ I ++ + L Sbjct: 830 GGQNAMIADSSALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAMLAGAMAEL 889 Query: 314 KLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVPKFGDARDAGFWVEPT 373 K+G P +T +GP+I + R ++ + +E ++ G V G + P Sbjct: 890 KVGDPAQLSTDVGPVIDEDARKILVDHAARMDQEAKKI---GEVALDPATTGNGTFFAPR 946 Query: 374 I--ITGLPQTARCIKEEVFGPICHV-----SPFDTEAEAIALANDTKYGLSATTWTGNLN 426 I GL R E+FGP+ HV S D + I N T YGL+ + + Sbjct: 947 AYEIPGLATLTR----EIFGPVLHVIRWKGSELDKVVDEI---NATGYGLTLGIHSRIDD 999 Query: 427 RGHRVSEAMRVGLSWVNSWFLRDL--RTPFGGVGLSGIG-REGGMHSL 471 + RVG +VN + + PFGG GLSG G + GG H L Sbjct: 1000 TVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSGTGPKAGGPHYL 1047 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: 1179 Number of extensions: 65 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 490 Length of database: 1074 Length adjustment: 40 Effective length of query: 450 Effective length of database: 1034 Effective search space: 465300 Effective search space used: 465300 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: 55 (25.8 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