Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 317 bits (813), Expect = 4e-91 Identities = 177/472 (37%), Positives = 273/472 (57%), Gaps = 6/472 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 FI +++ + K NPAT E LGTV GA E A+ AA +L W+ TA +R Sbjct: 15 FIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA-WRSKTAAQR 73 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 A+LR+ DL++E +E+L++L + + GKP S +I AA F +F++ + I + Sbjct: 74 SAILRRWHDLLMENQEDLALLMTAEQGKPLAESRG-EIAYAASFFEWFAEEAKRIYGDII 132 Query: 134 QMDDVALNYA-IRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 + I++PVGV+ I PWN P ++T K ALAAG T+V+KPA TP +A Sbjct: 133 PQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALA 192 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 +A++ ++AG+P GV N+V G ++ G LT +P V ++FTG T GK +M A T+K Sbjct: 193 IAKLAQEAGMPPGVFNVVTG-SSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCAGTMK 251 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 R+S ELGG P ++F D++LD +E + + N G+ C+C +R+YV+ Y+ F EK Sbjct: 252 RVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLA 311 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372 L VG+ + G LI + E V +I A+++G +L GGKR G F Sbjct: 312 RAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR--HALGGTFF 369 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 PT++ +T D V KEEIFGP + F++E EV+++ NDT YGL+A +T D+ R R Sbjct: 370 SPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWR 429 Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 V ++E G++ +N+ + + PFGG+K+SG GREG + + Y E+ +C+ Sbjct: 430 VGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481 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: 594 Number of extensions: 27 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 ( 7.3 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 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