Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Koxy:BWI76_RS10695 Length = 495 Score = 360 bits (925), Expect = e-104 Identities = 202/488 (41%), Positives = 287/488 (58%), Gaps = 8/488 (1%) Query: 2 QQTKVKPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL 61 Q+ + I+ FI+G++ + D F I+PA ++ L VA G A++D AVQAA+ Sbjct: 11 QKARELTIETRLFINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVDRAVQAARGVF 70 Query: 62 N-GPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHF 120 + G W + + +R AVL K DL+ +EEL++LE+LDTGKP S DIP AA + Sbjct: 71 DRGDWSQASPAQRKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDDIPGAARAIRW 130 Query: 121 FSDYIRTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVM 180 +++ I + E L +R P+GVI + PWN PLLL WKL PALA+GN+VV+ Sbjct: 131 YAEAIDKVYGEVAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGPALASGNSVVL 190 Query: 181 KPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTG 240 KP+E +P+TA LA + + AG+PDGV N+V GFG + AG AL HPDV I+FTG T T Sbjct: 191 KPSEKSPLTALRLAGLAKQAGLPDGVFNVVSGFG-HEAGQALALHPDVEVITFTGSTRTA 249 Query: 241 KIIMASAA-KTLKRLSYELGGKNPNVIFAD-SNLDEVIETTMKSSFINQGEVCLCGSRIY 298 K ++ A +KR+ E GGK+ N++FAD +L + + T F NQG+VC+ G+R+ Sbjct: 250 KQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQVCIAGTRLL 309 Query: 299 VERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILT 358 +E + FL+ + K G+P D T +G LI + H + V +I+ +L Sbjct: 310 LEESIADRFLDLLKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAGEAHSTLLLD 369 Query: 359 GGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGL 418 G K P G PTI + + +EEIFGPV+ V F EE+ L ND+ YGL Sbjct: 370 GRKNPWPAAVG----PTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALANDSRYGL 425 Query: 419 SASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 A+VWT DL RAHRV+ +++AG V+VN + D+ PFGG KQSG GR+ LH+ E ++E Sbjct: 426 GAAVWTRDLSRAHRVSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTE 485 Query: 479 LTNICIKL 486 L I I L Sbjct: 486 LKTIWIAL 493 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: 582 Number of extensions: 24 Number of successful extensions: 6 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: 495 Length adjustment: 34 Effective length of query: 452 Effective length of database: 461 Effective search space: 208372 Effective search space used: 208372 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