GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaA in Azospirillum brasilense Sp245

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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