Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q97YT9 (492 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 199 bits (507), Expect = 1e-55 Identities = 132/437 (30%), Positives = 208/437 (47%), Gaps = 11/437 (2%) Query: 36 NPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITTRIQYLFALKNRLEEYSETIA 95 NP + K +E+ +Q+A AF W + R L A+ +L E + I Sbjct: 7 NPTTGRVDYRHELLDKAGIEQRLQAAAGAFPAWSATSLQERAAVLRAIGAQLRERKDDIQ 66 Query: 96 RIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGEHLDQVSQEVDETVVREPLGVF 155 + + GK EA ++ + E A K + +D +Q V EP+G Sbjct: 67 GAMTREMGKLKVEALAEVEKCAAACEYYADHAADYLKPQLIDTEAQR--SYVRYEPIGCV 124 Query: 156 GIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPMDFIIRIFDEIKLPRGVVNVVH 215 + P+NFP F FL A + GN ++K + P D I + LP GV +V+H Sbjct: 125 FAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGVFDVLH 184 Query: 216 GAKDVVDEFLTNKLVQGVTFVGSTRVGKYIYENAGKNGKKAIVQAGAKNFVVVMPDADLN 275 D + L ++ V+ VT GS R G+ I NAG KK +++ G + VV+ DADL+ Sbjct: 185 IDNDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVVLDDADLD 244 Query: 276 KAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRKFIEASKQLKIGYGLDESVDMGPV 335 KAI + V + F N+GQ C+AA + V + D +F+ A+ + + G D + P+ Sbjct: 245 KAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADARTTLAPM 304 Query: 336 VTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPE--YPNGYFLGPTVFDEVTPEMVIAKE 393 D + + ++ + +GA++L G V YP TV D+V P M E Sbjct: 305 ARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYP------ATVLDQVGPGMPAYDE 358 Query: 394 EIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGYYARKFRREVNTGNIGINIGVA 453 E+FGPVA++I VK+ EA+ + N + +G S++TT F +++ G +N V Sbjct: 359 ELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSIVK 418 Query: 454 APMAFFPFGGRKESFFG 470 + + PFGG KES FG Sbjct: 419 SDVR-LPFGGSKESGFG 434 Lambda K H 0.319 0.139 0.398 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: 439 Number of extensions: 21 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: 492 Length of database: 454 Length adjustment: 33 Effective length of query: 459 Effective length of database: 421 Effective search space: 193239 Effective search space used: 193239 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 (21.7 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