Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 15565 b1444 medium chain aldehyde dehydrogenase (NCBI)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Keio:15565 Length = 474 Score = 330 bits (845), Expect = 8e-95 Identities = 187/473 (39%), Positives = 277/473 (58%), Gaps = 8/473 (1%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74 I+G+ V S +G+ NPAT + L +AE A ++D AV+AA A W + T R Sbjct: 7 INGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF-AEWGQTTPKVRA 64 Query: 75 AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQ 134 L K+ D+I E + + LES + GKP + + +IP F FF+ R + A Sbjct: 65 ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124 Query: 135 MDDVALNYAIRR-PVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 IRR P+GV+ I PWN PL++ WKLAPALAAGN VV+KP+E+TP+TA L Sbjct: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253 AE+ +D P GV+N++ G G + G LT HP V +S TG TG+ I++ A ++KR Sbjct: 185 AELAKDI-FPAGVINILFGRG-KTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKR 242 Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313 ELGGK P ++F D++++ V+E + N G+ C RIY ++ Y+ +EK A Sbjct: 243 THMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGA 302 Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGT-ILTGGKRPEGLEKGYFL 372 L G P D T++G L S H ERV ++ A G ++TGG++ +G GY+ Sbjct: 303 AVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG--NGYYY 360 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 PT++ G +D +V++E+FGPVV+V PFD EE+V+ ND+ YGL++SVWT D+ RAHR Sbjct: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420 Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIK 485 V+ +++ G WVNT F+ P GG K SG G++ L+ E Y+ + ++ +K Sbjct: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 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: 569 Number of extensions: 25 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: 474 Length adjustment: 34 Effective length of query: 452 Effective length of database: 440 Effective search space: 198880 Effective search space used: 198880 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: 51 (24.3 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