Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 237 bits (604), Expect = 7e-67 Identities = 141/429 (32%), Positives = 217/429 (50%), Gaps = 9/429 (2%) Query: 48 AEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSG 107 A I+ +QAA A W + ER AVLR +G + ERK+++ + + GK + Sbjct: 23 AGIEQRLQAAAGAFPA-WSATSLQERAAVLRAIGAQLRERKDDIQGAMTREMGKLK-VEA 80 Query: 108 SIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWK 167 ++ + A +++D+ + +Y P+G + + PWN P+ + Sbjct: 81 LAEVEKCAAACEYYADHAADYLKPQLIDTEAQRSYVRYEPIGCVFAVMPWNFPIWQVFRF 140 Query: 168 LAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPD 227 LAPA AGN ++K A P A ++ E+ R G+PDGV +++H N A + Sbjct: 141 LAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGVFDVLHI--DNDQAADVLRDRR 198 Query: 228 VNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQ 287 V A++ TG G+ I A+A LK+ ELGG + V+ D++LD+ I+ +KS F N Sbjct: 199 VKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVVLDDADLDKAIDAAVKSRFDNS 258 Query: 288 GEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIK 347 G+ C+ R V +AF E+FVA E GDP DA+T + + + + + ++ Sbjct: 259 GQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADARTTLAPMARADLRDELHKQVQ 318 Query: 348 LAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEV 407 +V +G +L GG+ +G GY T++ + EE+FGPV VI E E Sbjct: 319 ASVAKGARVLAGGEPVDGSHAGY--PATVLDQVGPGMPAYDEELFGPVAAVIRVKDEAEA 376 Query: 408 LEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGR- 466 L+ NDT +GL SVWT D R A Q+E G +VN+ D+R PFGG K+SG GR Sbjct: 377 LKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSIVKSDVRLPFGGSKESGFGRE 436 Query: 467 --EGGLHSF 473 E G+H F Sbjct: 437 LAEHGIHEF 445 Lambda K H 0.318 0.136 0.404 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: 480 Number of extensions: 17 Number of successful extensions: 4 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: 486 Length of database: 454 Length adjustment: 33 Effective length of query: 453 Effective length of database: 421 Effective search space: 190713 Effective search space used: 190713 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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