Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 350 bits (898), Expect = e-101 Identities = 190/483 (39%), Positives = 286/483 (59%), Gaps = 23/483 (4%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGP-WKKMTANER 73 I G P+L G+ +PATE + + AA+I AV +A++A + W+ + +R Sbjct: 26 IGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADR 85 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 +L ++ +LI +ELS LE+L +GK ++ +ID+ A +++R + AT Sbjct: 86 EKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGA-------EFVRYMAGWAT 138 Query: 134 QMDDVALN------------YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMK 181 +++ L+ Y R PVGV+G I PWN PL + WK+APALAAG TVV+K Sbjct: 139 KLEGQTLDNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLK 198 Query: 182 PAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGK 241 P+E TP+TA LA + +AG+P+GV+N+V G G +AGAAL HP V +SFTG T GK Sbjct: 199 PSEDTPLTALRLAHLALEAGIPEGVLNVVCGRGA-TAGAALIAHPGVRKLSFTGSTAVGK 257 Query: 242 IIMASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVER 301 ++ +A + + R + ELGGK+P V+ D++ +V + F +QG+VC SR+ V R Sbjct: 258 VVGHAAVENMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHR 317 Query: 302 PAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK 361 Y L++ + + +G FDA T+ G L S H+ RV +I A EG T++ GG+ Sbjct: 318 SLYRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGE 377 Query: 362 RPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSAS 421 R + G F++PTI T RVV+EE+FGPV+ V PFD E+ + NDT YGL+AS Sbjct: 378 RVH--DAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAAS 435 Query: 422 VWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTN 481 +WT L AHR+ +++AG+VWVN + D P GG+KQSG GR+ G + E ++EL + Sbjct: 436 LWTQSLSHAHRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKS 495 Query: 482 ICI 484 +C+ Sbjct: 496 VCM 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: 580 Number of extensions: 17 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: 500 Length adjustment: 34 Effective length of query: 452 Effective length of database: 466 Effective search space: 210632 Effective search space used: 210632 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