Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 313 bits (803), Expect = 7e-90 Identities = 177/482 (36%), Positives = 260/482 (53%), Gaps = 10/482 (2%) Query: 5 KHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVA 64 K + GA+ + SG TF NP+ G VI HV + GRAE A+ AA AA K PW + Sbjct: 21 KAYFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQK-PWAARTAK 79 Query: 65 ERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANE 124 +RA++L R D I D+ + GKP + A ++ GA+ + FA+ K + E Sbjct: 80 DRAQVLRRWFDLIVGNADDLARILTAEMGKPLAEARG-EVMYGASFVEWFAEEAKRLYGE 138 Query: 125 AFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETP 184 PD + +R+P GV+G I+PWN P+ ++T K PALA G + KP+E+TP Sbjct: 139 TIPGHLPDARIQV---IRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTP 195 Query: 185 LTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAA 244 L+A L + + AG+PAG++ V+ + G E+ V TFTG T G +++ A Sbjct: 196 LSALALAVLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQA 255 Query: 245 AKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEF 304 A V++ S+ELGG IVF D D+DKA+EG + F N GQ C+ R+YV+ ++D F Sbjct: 256 ADQVKKCSMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAF 315 Query: 305 VARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPA 364 +L A E L +G GPL+++ EKV + GG+V+TGG Sbjct: 316 AEKLAAAVEELKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGG-----ET 370 Query: 365 HLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWT 424 H GG + PT+ TG++ + V EE FGP + F E+E I +AN +GLA + Sbjct: 371 HPLGGTFFTPTVVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYA 430 Query: 425 ENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICV 484 + R RV+ +E GIV +N+ + FGG KQSG+GREG H ++ Y E+K IC+ Sbjct: 431 RDIGRITRVSEALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICL 490 Query: 485 KL 486 + Sbjct: 491 SI 492 Lambda K H 0.318 0.136 0.411 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: 626 Number of extensions: 32 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: 486 Length of database: 492 Length adjustment: 34 Effective length of query: 452 Effective length of database: 458 Effective search space: 207016 Effective search space used: 207016 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: 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