Align 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized)
to candidate WP_086509800.1 BZY95_RS10050 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::P23105 (486 letters) >NCBI__GCF_002151265.1:WP_086509800.1 Length = 485 Score = 314 bits (805), Expect = 4e-90 Identities = 181/482 (37%), Positives = 269/482 (55%), Gaps = 14/482 (2%) Query: 7 FISGELVGSASGKLFDNVSPANGQVIGRVHEAGRAEVDAAVRAARAALKGPWGKMTVAER 66 +I G V + SG+ + V+PA G+ G V GRAE + A+ AA AAL G W +T ER Sbjct: 15 YIDGSWVAADSGEQIEVVNPATGETFGTVPRLGRAETERAIAAADAALVG-WRALTAQER 73 Query: 67 AEILHRVADGITARFGEFLEARMPGHRQAEVAGQPHRHSARRANF-KVFADLLKNVANEA 125 A+IL + D + + A + H Q + + A A+F + FA+ + + E Sbjct: 74 ADILMKWHDLMMEHQDDL--AMIMTHEQGKPLKEAAGEIAYAASFLRWFAEEARRIYGET 131 Query: 126 FEMATPDGAGALNYGVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNCVVVKPSEETPL 185 A P+ + ++P GV+G I+PWN P ++T K G ALA G +V+KP+ +TP Sbjct: 132 IPAAKPNQRIVVT---KQPVGVVGAITPWNFPAAMITRKAGAALAAGCTIVIKPASQTPF 188 Query: 186 TATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGETIMRAAA 245 +AT L + + AG+P GV+NVV G + A A +TE P V TFTG T G +M A+ Sbjct: 189 SATALALLAERAGIPRGVFNVVPGRASEIASA-MTESPLVRKITFTGSTEVGRELMAQAS 247 Query: 246 KGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDAFV 305 + ++++SLELGG IVF D D+D A+EG + + F N GQ C+ T R V+ + +AF Sbjct: 248 RHIQKISLELGGNAPFIVFEDADLDAAVEGAMAAKFRNAGQTCICTNRFLVQSSVINAFC 307 Query: 306 ARLKAGAEA-LKIGEPNDPEANFGPLISHKPREKVPSYYQQAVDDGATVVTGGGVPEMPA 364 +L + LK+G+ +P+ N GPLI K KV + AVD GA ++ GG Sbjct: 308 EKLAVAMNSELKVGDGTEPDINIGPLIDEKAVAKVSEHVHDAVDKGAELLLGGN-----P 362 Query: 365 HLAGGAWVQPTIWTGLADDSAVVTEEIFGPCCHIRPFDSEEEAIELANSLPYGLASAIWT 424 H GG + PT+ + D V EE FGP + PF+ EE+A+++AN YGLAS ++ Sbjct: 363 HPLGGNFFSPTLISFANADMKVAHEETFGPLAAVFPFEDEEDAVQMANDTQYGLASYFYS 422 Query: 425 ENVRRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICV 484 ++ R RVA +E G+V +N+ + + FGG K SG+GREGG +E + E K +C+ Sbjct: 423 RDLGRVWRVADALEYGMVGINTGLISNTAAPFGGVKASGLGREGGHQGIEEFLETKYLCI 482 Query: 485 KL 486 L Sbjct: 483 DL 484 Lambda K H 0.318 0.136 0.413 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: 549 Number of extensions: 26 Number of successful extensions: 5 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: 486 Length of database: 485 Length adjustment: 34 Effective length of query: 452 Effective length of database: 451 Effective search space: 203852 Effective search space used: 203852 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: 52 (24.6 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