Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 227 bits (578), Expect = 7e-64 Identities = 143/461 (31%), Positives = 231/461 (50%), Gaps = 13/461 (2%) Query: 22 VNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTVAERAAILCRIADEIDRRYDD 81 VNP G V + D+ ++ ++A A AW T++ ERAA+L I ++ R DD Sbjct: 6 VNPTTGRVDYRHELLDKAGIEQRLQAAAGAFP-AWSATSLQERAAVLRAIGAQLRERKDD 64 Query: 82 FLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPLDTFQTDLPDGARALNYAVRK 141 A + GK + + + ++ + AA +AD D + L D +Y + Sbjct: 65 IQGAMTREMGK-LKVEALAEVEKCAAACEYYAD----HAADYLKPQLIDTEAQRSYVRYE 119 Query: 142 PLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGTATLLAEVMHTVGVPPGV 201 P+G V + PWN P+ + +APA GN + K + P A L+ EV+ G+P GV Sbjct: 120 PIGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGV 179 Query: 202 FNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAATHVKPVSFELGGKNAAII 261 F+++H D A + + + + A+T TG R G +I A +K ELGG +A ++ Sbjct: 180 FDVLH-IDNDQAAD-VLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVV 237 Query: 262 FADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLDAFVERVKALKLGWPQDG 321 D D +K ID +++ F +SGQ C+ A+R V + + F + FV + G P D Sbjct: 238 LDDADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADA 297 Query: 322 TTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVPKFGDARDAGFWVEPTIITGLPQT 381 T + P+ A+ RD++ + + +GA+VL GG + D AG+ T++ + Sbjct: 298 RTTLAPMARADLRDELHKQVQASVAKGARVLAGG---EPVDGSHAGY--PATVLDQVGPG 352 Query: 382 ARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGNLNRGHRVSEAMRVGLSW 441 EE+FGP+ V EAEA+ +ANDT++GL + WT + RG ++ M G ++ Sbjct: 353 MPAYDEELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAF 412 Query: 442 VNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYSELTNVCV 482 VNS D+R PFGG SG GRE H ++ + + + V Sbjct: 413 VNSIVKSDVRLPFGGSKESGFGRELAEHGIHEFMNIKTIYV 453 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: 540 Number of extensions: 28 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: 454 Length adjustment: 33 Effective length of query: 457 Effective length of database: 421 Effective search space: 192397 Effective search space used: 192397 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: 51 (24.3 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