GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroD in Chromobacterium vaccinii MWU205

Align arginine oxidase (EC 1.4.3.25) (characterized)
to candidate WP_046157805.1 VL52_RS15120 FAD-dependent oxidoreductase

Query= metacyc::MONOMER-11561
         (589 letters)



>NCBI__GCF_000971335.1:WP_046157805.1
          Length = 539

 Score =  284 bits (726), Expect = 7e-81
 Identities = 203/564 (35%), Positives = 286/564 (50%), Gaps = 86/564 (15%)

Query: 8   DVAIIGGGVSGTYSAWRLQEAQGDHQRIQLFEYSDRIGGRLFSINLPGLPNVVAEVGGMR 67
           D+AI+GGGVSG Y AWRL++     Q+I +FE SD IGGRL S+  P +P++VAE+GGMR
Sbjct: 7   DIAIVGGGVSGVYCAWRLKQTNPG-QKIAVFEASDHIGGRLLSVRPPDIPDMVAELGGMR 65

Query: 68  WMPATDDNTGGHVMVDKLVGELKLESKNFPMGSNLP-EKDPVGAKDNLFYLRGERFRLRD 126
            +PA         +V KL+ EL  E    P    +   K PV    N+ +LRG   RL D
Sbjct: 66  ILPAVQP------LVTKLITELNQE---LPADEQITLYKFPVDEPQNIAFLRGVYLRLAD 116

Query: 127 FTEAPDKIPYKLAWSERGFGPEDLQVKVMNNIYPGFDKLSLAEQMQ------VKVFGKEI 180
           FT  PD +PY+L + + G    ++ V  +  I PG    +L E+ +       +  G  +
Sbjct: 117 FTNDPDIVPYQLNFIDHGQSAGEVIVNAIEQIVPGITNPNLNEEQRREMAQSAEFGGVPL 176

Query: 181 WRYGFWDLLYRVLSNEGYQFMKDAGGYEANVANASAVTQLP--ATEYSDKTIFLTLKKGF 238
           ++ GFW++L RV++ E Y + +D GGY++ + N +A   +P   +++     ++    GF
Sbjct: 177 YKQGFWNVLLRVITGEAYHYAEDVGGYDSTLCNWNAADAIPWYLSDFGVSPEYMGFCNGF 236

Query: 239 QALPLTLAQRFAEVPGGLVPGEQRIRMNRRLASVQFSDDTEYPYRLHF-QATRTIDGKTS 297
           Q +PL+LAQ F E  GG V          RLAS             H    T   DG   
Sbjct: 237 QQVPLSLAQLF-EKSGGDV----------RLAS-------------HISHITLQGDGFAF 272

Query: 298 DVPGAEEIVHARQVILALPRRSLELI--QSPLFDDPWLKENIDSVLVQSAFKLFLAYEQP 355
            V G+     A+++ILA+PRRSLEL+   SP   D   +  I +V  +  FKLF  Y+ P
Sbjct: 273 QVNGS--AATAKKLILAMPRRSLELLTATSPALQDAKTQALISTVTPRPLFKLFTTYDSP 330

Query: 356 WWRSQG--------------LVAGRSVTDLPIRQCYYMGTECEQDGGEKTL-NSLLMASY 400
           WWR+ G              + AGRSVTDLP+RQ YY     + DG   T  +++L+ASY
Sbjct: 331 WWRNTGYSSTDAKGEPIYVAVQAGRSVTDLPVRQTYYWP---KSDGTAATEGHAMLLASY 387

Query: 401 NDIGTVPFWKGLEDGAPFEGYQPKSLLGR-----------VDAN---EVVPKMQYQISEE 446
           +D     FW    DG   +  QP++ LGR           VD N   + +   QY+    
Sbjct: 388 DDGDNTGFW----DGLRAKRRQPRA-LGRDVAPLADPFIGVDDNVQRDELEWHQYKAPRM 442

Query: 447 MVRIAQRQVTSLHDQIELPAPYSAVYHAWDADPFGGGWHEWKANYRLDLIIQRMRHPVQE 506
           M     RQ+T +H     P   +A Y  W  DPFGGGW+ W    +   +   +  P  +
Sbjct: 443 MTEEVTRQLTVMHSLNYTPKVRNAAYRDWGDDPFGGGWNSWNIGVKSWEVKHAVVQPT-D 501

Query: 507 QEVYIVGEAYSYGQGWVEGALTTA 530
             +YI GEAYS  QGWVEGAL TA
Sbjct: 502 LPLYICGEAYSDAQGWVEGALQTA 525


Lambda     K      H
   0.319    0.137    0.422 

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: 938
Number of extensions: 59
Number of successful extensions: 11
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: 589
Length of database: 539
Length adjustment: 36
Effective length of query: 553
Effective length of database: 503
Effective search space:   278159
Effective search space used:   278159
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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