Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate AZOBR_RS16155 AZOBR_RS16155 altronate hydrolase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__azobra:AZOBR_RS16155 Length = 495 Score = 545 bits (1403), Expect = e-159 Identities = 280/496 (56%), Positives = 344/496 (69%), Gaps = 5/496 (1%) Query: 2 QYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLP 61 +Y+KIH+ D VAVAL LA+GT ++D + L +V +GHKFA+T G VIKYG Sbjct: 3 KYLKIHSSDTVAVALEPLAQGT--AIDGLGIVLLDEVPQGHKFAVTPHQPGDRVIKYGSV 60 Query: 62 IGYALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDL-PAQAADREVQIYRRANGDVGV 120 IG A I G H+H HN T L L Y Y D PA+ +Q + RANG+VGV Sbjct: 61 IGLAKEAIPVGRHIHTHNIGTALGGLQNYAYAGPANDAAPAKREAPTIQAFVRANGEVGV 120 Query: 121 RNELWILPTVGCVNGIARQIQNRFLKETNNAEGTDGVFLFSHTYGCSQLGDDHINTRTML 180 RN+LWI+P VGCVNG+A+ RF K EG+ V + H YGCSQLG D NTR +L Sbjct: 121 RNDLWIIPLVGCVNGLAKNAAKRFEKMGLLPEGSR-VMVLEHPYGCSQLGGDLDNTRNIL 179 Query: 181 QNMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQQDDEIEAGIEHLHQ 240 ++ HPNAG VLV+GLGCENN A F + DP R+ ++ Q+ DE+EA +E + + Sbjct: 180 RDFAIHPNAGGVLVMGLGCENNTRALFTQGFEHPDPRRLRYLTTQEVSDELEASLEAMTE 239 Query: 241 LYNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVLTEVPE 300 L VMR DKREP L+ GL+CGGSDG SGITANP+LG SD++ GG TVLTEVPE Sbjct: 240 LAAVMREDKREPVGADRLRIGLKCGGSDGFSGITANPLLGALSDWLCGIGGATVLTEVPE 299 Query: 301 MFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTLEDKSL 360 MFGAE LLM+ F+ +VT++NDFKQYFI H+QPIYENPSPGNKAGGI+TLE+KSL Sbjct: 300 MFGAEHLLMERAESREVFDGVVTLINDFKQYFIDHNQPIYENPSPGNKAGGISTLEEKSL 359 Query: 361 GCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTGRGTPY 420 GCTQKAG S V DV+RY ER++ PGL LL APGND VA +ALA AGCH+VLF+TGRGTP Sbjct: 360 GCTQKAGLSPVRDVIRYAERIRKPGLTLLEAPGNDGVAVTALAAAGCHIVLFTTGRGTPL 419 Query: 421 GGFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKA-MPQLLEEFIDTIVEFANGKQTCNE 479 GG VPT+KIATN+ +A KK+HWIDF+AG + A + LL FID+I+ ANGK+ NE Sbjct: 420 GGVVPTMKIATNTAMAEKKRHWIDFNAGPIAEATATVDSLLPSFIDSILAVANGKEARNE 479 Query: 480 RNDFRELAIFKSGVTL 495 ND +L IFKSGVTL Sbjct: 480 ENDVHDLVIFKSGVTL 495 Lambda K H 0.319 0.136 0.403 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: 750 Number of extensions: 27 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: 495 Length of database: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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