Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 351 bits (900), Expect = e-101 Identities = 185/474 (39%), Positives = 280/474 (59%), Gaps = 6/474 (1%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 HFIDG +V G I PAT E++ TV A +D A+ AA +A W M+ E Sbjct: 11 HFIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKA-WAAMSGTE 69 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +LR+ D++ ER +LSVLE+ DTGKP + ++D A +F ++T E Sbjct: 70 RGRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEH 129 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 Q+ + + Y R P+GV I WN P + WK APALA GN +V KP+E TP+ A Sbjct: 130 IQLGEDWV-YTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALK 188 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 +AEI +AG+P G+ N+V G G GA+L P V +S TG TGK + A+AA+ +K Sbjct: 189 VAEILHEAGLPAGIYNVVQGLG--EVGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMK 246 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 ++ ELGGK+P +IF D++L+ + + +F + G+VC G+R++V++ EAFL++ Sbjct: 247 HVTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLT 306 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372 + VVGDP D T G ++S++ + V YI+ EG ++ GG+R G++L Sbjct: 307 ERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLN--RDGFYL 364 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 +PT+ + D + +EEIFGPV+ V+ F+TEEE + + N T +GLSA V+T DL RAHR Sbjct: 365 QPTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHR 424 Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 V Q+EAG ++N++ + PFGG K SG+GRE + YSE+ ++ +++ Sbjct: 425 VIAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVRM 478 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: 577 Number of extensions: 29 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 Sep 24 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