Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 403 bits (1035), Expect = e-117 Identities = 208/476 (43%), Positives = 299/476 (62%), Gaps = 4/476 (0%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL-NGPWKKMTANE 72 +IDG++ + DG TF+ INPAT + L VA GA ++D AV AA+KA +G W + Sbjct: 24 YIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAAARKAFQSGVWSDTPRSA 83 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R A L ++ LI +EEL++LE+LD GKP + DIP A + ++++ I I +E Sbjct: 84 RKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAGRTYAWYAEAIDKIYDEI 143 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 L R P+GV+ + PWN PLL+ +WK+APALAAGN+VV+KPAE +P+TA Sbjct: 144 APTGPGVLATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGNSVVLKPAEQSPLTALR 203 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA-SAAKTL 251 LAE+ +AG+P GV N+V G G +AG AL HPDV+ I+FTG T TGK M S L Sbjct: 204 LAELAEEAGIPAGVFNVVPGLGA-AAGQALGRHPDVDCIAFTGSTATGKRFMEYSGQSNL 262 Query: 252 KRLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEK 310 KR+ E GGK+P+++F D +LD + F NQGE+C+ GSR+YV+ Y+AF+EK Sbjct: 263 KRVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGSRLYVQSGIYDAFMEK 322 Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGY 370 A + GDP D T +GA++ +RV Y+K +EG + GGKR G+ Sbjct: 323 LEAHAARMQPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEGARLRAGGKRAHTDSGGF 382 Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430 +++PTI T+ +V+EEIFGPV+ V F++EEE + ND+ YGL + +WT++L RA Sbjct: 383 YMQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSPYGLGSGLWTSNLSRA 442 Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 HRV+ +++AG+VWVN + D+ PFGG+KQSG GR+ LH+ + Y++L I L Sbjct: 443 HRVSRKLQAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALDKYTDLKTTWISL 498 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: 605 Number of extensions: 24 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: 499 Length adjustment: 34 Effective length of query: 452 Effective length of database: 465 Effective search space: 210180 Effective search space used: 210180 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