Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4184 Length = 498 Score = 330 bits (847), Expect = 5e-95 Identities = 182/473 (38%), Positives = 270/473 (57%), Gaps = 7/473 (1%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74 I+G++V + FD +PAT KL VA G A+ + A+ AA A GPWK TA ER Sbjct: 23 INGQWV--VGSSRFDVNDPATGLKLADVANLGPADAEAAIAAANAAW-GPWKTKTAKERS 79 Query: 75 AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT- 133 +LRK DL++ +++L + + + GKP ++ A +F++ + I E Sbjct: 80 IILRKWFDLLMANQDDLGRIMTAEQGKPL-AEAKGEVAYGASFVEWFAEEAKRINGETLP 138 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 Q D+ +++P+GV I PWN PL ++T K+APALAAG VV+KPAELTP+TA Sbjct: 139 QFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPAELTPLTALAA 198 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSA--GAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 AE+ AG+P GV N++ NS G L V ISFTG T G+I+MA +A T+ Sbjct: 199 AELAIRAGIPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSAPTV 258 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 K++S ELGG P ++F D+++D +E S + N G+ C+C +R YV+ Y+ F+ KF Sbjct: 259 KKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQEGVYDEFVAKF 318 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371 AK K VG+ F+A G LI + +V ++ A+ +GG ++ GG+R L G F Sbjct: 319 AAKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGGQRLTALGSGQF 378 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 EPT++ T D +EE FGP V F TE+E ++ N+T +GL++ ++ D+ R Sbjct: 379 FEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLASYFYSRDVGRIF 438 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 RV +E G+V N L PFGG+KQSG+GREG H + Y E+ +C+ Sbjct: 439 RVTEALEYGMVGANVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIKYLCL 491 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: 608 Number of extensions: 28 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: 498 Length adjustment: 34 Effective length of query: 452 Effective length of database: 464 Effective search space: 209728 Effective search space used: 209728 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