Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate RR42_RS27835 RR42_RS27835 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Cup4G11:RR42_RS27835 Length = 486 Score = 434 bits (1116), Expect = e-126 Identities = 228/479 (47%), Positives = 311/479 (64%), Gaps = 11/479 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 H+I+GK V S D TF NPAT E++ TVA GG AE++ AV AAK A W A E Sbjct: 4 HWINGKQVDSKD--TFTTWNPATGEEIATVAAGGEAEVNAAVAAAKAAFP-KWANTPAKE 60 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R ++R++ DLI E L+ LE+ DTG P +G IPRAA NF+FF++ + Sbjct: 61 RARIMRRLADLITEHVPHLAALETQDTGLPIAQTGKQLIPRAAENFNFFAEVCVQMNGRT 120 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +DD LNY + +PVGV LI+PWN+P + TWK+AP LA GNT V+K +EL+P+TA Sbjct: 121 YPVDDQMLNYTLYQPVGVCALISPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTADQ 180 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L + +AGVP GV+N+V G+G SAG AL HPDV A+SFTG T TGK I+ A LK Sbjct: 181 LGMLALEAGVPAGVLNVVQGYGA-SAGDALVRHPDVRAVSFTGGTATGKRIIERAG--LK 237 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 + S ELGGK+P ++F D++L+ ++ + + F GE C GSRI+V+ Y+ F KF Sbjct: 238 KFSMELGGKSPVLVFDDADLERALDAALFTIFSINGERCTAGSRIFVQDTVYDDFAGKFA 297 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR-----PEGLE 367 + + L VGDP +T VGA+I+ +H+E+VTGYI+L +EG TIL GG P L Sbjct: 298 ERARRLRVGDPTSEQTHVGAMITQQHWEKVTGYIRLGEQEGATILAGGAERPSDLPAHLR 357 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 G F++PT++ + RV +EEIFGPV +IPF E++ L NDT YGL++ +WT D+ Sbjct: 358 NGNFVQPTVLANVENHMRVAQEEIFGPVACLIPFKGEDDGLAMANDTAYGLASYIWTQDV 417 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 + HR+A IEAG+V+VN+ +RDLR PFGG K SG GREGG SFE ++E+ N+CI + Sbjct: 418 GKVHRLARGIEAGMVFVNSQNVRDLRQPFGGTKASGTGREGGEFSFEVFAEVKNVCISM 476 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: 631 Number of extensions: 31 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: 486 Length adjustment: 34 Effective length of query: 452 Effective length of database: 452 Effective search space: 204304 Effective search space used: 204304 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