GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adiA in Chromobacterium vaccinii MWU205

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_046156677.1 VL52_RS08800 arginine/lysine/ornithine decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>NCBI__GCF_000971335.1:WP_046156677.1
          Length = 752

 Score =  528 bits (1360), Expect = e-154
 Identities = 291/769 (37%), Positives = 439/769 (57%), Gaps = 41/769 (5%)

Query: 4   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63
           ++I++ +F  ++T  G+ +  LA A+  + ++VI  TS+ D  +           + S  
Sbjct: 7   IVIIDEDFRSENT-SGSGIRELAAAMEAEGMSVIGYTSYGDLTSFAQQQSRAAGFILSID 65

Query: 64  MEQPDEHLSVRQLIGKLH-------ERQQNVPVFLLGDREKATASLDRDLLELVDEFAWI 116
            E+     S ++ +G L+        R  ++PV+L G+   A   +  D+L  +  F  +
Sbjct: 66  DEEFQTVDSAQESLGNLYGFVAEIRRRNPDIPVYLYGETRTAR-HIPNDILRELHGFIHM 124

Query: 117 LEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGR 176
            EDT +F+A   +     Y   L PP F AL+ Y+    YSW  PGH GGV F K+P G+
Sbjct: 125 HEDTPEFVARHIIREAKSYLDNLAPPFFRALVDYAYDGSYSWHCPGHSGGVAFLKSPVGQ 184

Query: 177 FYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNR 236
            +H ++GEN+ R+D+      LG LLDHTG    SE+NAAR+F AD  + V  GTS SN+
Sbjct: 185 MFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNADHLFFVTNGTSTSNK 244

Query: 237 TIMQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETL 296
            +  +C+   D+V++DRNCHKS    +I+TGA PV+++P+RN YGIIGPI   E QP+T+
Sbjct: 245 IVWHSCVAAGDIVLVDRNCHKSNLHAIIMTGAIPVFLMPTRNHYGIIGPIPKSEFQPDTI 304

Query: 297 QKKISASP----LTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWY 352
           +KKI A+P    + + +  +KP    +T  TYDG+ YN +E + LL    D +HFDEAW 
Sbjct: 305 KKKILANPFAREMLEQRPNRKPRILTLTQSTYDGILYNVEEIKGLLDGEVDTLHFDEAWL 364

Query: 353 GYARFNPIYCDHYAM-RGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRG-AVNFS 410
            +A F+  Y D +A+  G P   +   VF+T STHKLL  +SQAS I V++ +   ++ +
Sbjct: 365 PHACFHDFYRDFHAIGEGRPRCEDS-LVFSTQSTHKLLAGISQASQILVQDPQNRQLDTA 423

Query: 411 RFNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFT 470
            FN+AY+MH +TSP Y+I AS DVA +MM+   G SL +E + EA++FR+AM ++ +E+ 
Sbjct: 424 WFNEAYLMHTSTSPQYSIIASCDVAAAMMEQPGGQSLVEESLVEAMEFRRAMRKVDEEY- 482

Query: 471 DEGDWFFKPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWS 530
              DW+F  W  D ++D                   DQ  W +RP E WHGF  + D ++
Sbjct: 483 -GRDWWFSVWGPDDLSDDG---------------ICDQTDWTLRPDERWHGFAGIEDGFN 526

Query: 531 MLDPIKVSILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRG 590
           MLDPIK ++L PG+  DG  E  G+PAA+VT +L  HG+V  +T  +    +F++G+T+G
Sbjct: 527 MLDPIKATVLTPGLDVDGSFEEMGIPAAIVTKYLTEHGVVVEKTGLYSFFIMFTIGITKG 586

Query: 591 KWGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGA 650
           +W TLI+ L  FK  +D N PL +VMPE V  YP  Y  +G+ DL  ++     +++   
Sbjct: 587 RWNTLISLLQQFKDDFDKNQPLWRVMPEFVAKYPQ-YDRVGLQDLCQRIHGLYTKHDVAR 645

Query: 651 RLNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGEN 710
                Y +     + P DA+  + +  IE V ++ L GR+ A  + PYPPGIP+L+ GE 
Sbjct: 646 LTTDIYLSDMEPAMRPADAFAKMAHREIERVPVDQLEGRVTAVLLTPYPPGIPLLIPGER 705

Query: 711 FGDENSPQVGYLRSLQSWDHHFPGFEHETEGTEIID----GVYHVMCVK 755
           F   N   V YLR  Q+++   PGFE +  G   ++     VY V CVK
Sbjct: 706 F---NKTIVDYLRFAQAFNRELPGFETDVHGLVAVEVQDRKVYCVDCVK 751


Lambda     K      H
   0.319    0.135    0.415 

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: 1458
Number of extensions: 80
Number of successful extensions: 8
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: 756
Length of database: 752
Length adjustment: 40
Effective length of query: 716
Effective length of database: 712
Effective search space:   509792
Effective search space used:   509792
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 (21.8 bits)
S2: 55 (25.8 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