Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 352 bits (902), Expect = e-101 Identities = 198/482 (41%), Positives = 282/482 (58%), Gaps = 16/482 (3%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI G++V DG+ FDN +P K+ +A A +I+ A+ AA A G W + +A + Sbjct: 21 NFIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAAKAG-WARTSAAD 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L ++ D + E L+ E+ D GKP + + DIP A +F +F+ +R+ Sbjct: 80 RSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLRSQEGSI 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +++D + Y P+GV+G I PWN PLL+ WKLAPALAAGN VV+KPAE TP + V Sbjct: 140 SEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIMV 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 AE+ D +P GV+N+V+GFG AG L P + I+FTGET+TG++IM AA+ L Sbjct: 200 WAEMIGDL-LPAGVLNIVNGFG-LEAGKPLASSPRIAKIAFTGETSTGRLIMQYAAQNLI 257 Query: 253 RLSYELGGKNPNVIF------ADSNLDEVIE-TTMKSSFINQGEVCLCGSRIYVERPAYE 305 ++ ELGGK+PN+ F D LD+ +E TM + +NQGEVC C SR V+ YE Sbjct: 258 PVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFA--LNQGEVCTCPSRALVQESIYE 315 Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR--- 362 F+E+ + + +V G P D T +GA S+E ++ GY+ + EG +L GG+R Sbjct: 316 KFMERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRKIL 375 Query: 363 PEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASV 422 P L GY++EPT+ G + R+ +EEIFGPV+ V F TEEE LE NDT +GL A V Sbjct: 376 PGQLADGYYVEPTVFEGHNK-MRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAGV 434 Query: 423 WTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 W+ D R +R IEAG VW N + FGG KQSG+GRE + Y + N+ Sbjct: 435 WSRDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTKNM 494 Query: 483 CI 484 + Sbjct: 495 LV 496 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: 609 Number of extensions: 41 Number of successful extensions: 7 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: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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