Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 290 bits (741), Expect = 1e-82 Identities = 171/480 (35%), Positives = 254/480 (52%), Gaps = 12/480 (2%) Query: 7 YINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTVAER 64 Y G W + S F NP G V+A V + R AI A AA + W T +R Sbjct: 23 YFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQK-PWAARTAKDR 81 Query: 65 AAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPLDTF 124 A +L R D I DD A+ GKP+A A ++ GA+ FA+ K +T Sbjct: 82 AQVLRRWFDLIVGNADDLARILTAEMGKPLAEARG-EVMYGASFVEWFAEEAKRLYGETI 140 Query: 125 QTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGT 184 LPD A +R+P+GVVG I+PWN P+ ++T K APALA G A ++KP+E+TP + Sbjct: 141 PGHLPD---ARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLS 197 Query: 185 ATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAAT 244 A LA + G+P G+F ++ + G+ N + +TFTG ++ G ++ AA Sbjct: 198 ALALAVLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAAD 257 Query: 245 HVKPVSFELGGKNAAIIFADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLD 304 VK S ELGG I+F D D +K ++G M F ++GQ C+CA R+YV+ +Y+ F + Sbjct: 258 QVKKCSMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAE 317 Query: 305 AFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVPKFGDAR 364 V+ LK+G +GPLI+ +KV + R +G V+ GG G Sbjct: 318 KLAAAVEELKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLG--- 374 Query: 365 DAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGN 424 G + PT++TG+ Q + +EE FGP+ + F E E IA+ANDT +GL+ + + Sbjct: 375 --GTFFTPTVVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARD 432 Query: 425 LNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYSELTNVCVRI 484 + R RVSEA+ G+ +N+ + PFGGV SG+GREG H ++ Y E+ +C+ I Sbjct: 433 IGRITRVSEALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICLSI 492 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: 628 Number of extensions: 30 Number of successful extensions: 4 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: 492 Length adjustment: 34 Effective length of query: 456 Effective length of database: 458 Effective search space: 208848 Effective search space used: 208848 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