GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Chromobacterium vaccinii MWU205

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_046156677.1 VL52_RS08800 arginine/lysine/ornithine decarboxylase

Query= BRENDA::H8ZI01
         (721 letters)



>NCBI__GCF_000971335.1:WP_046156677.1
          Length = 752

 Score =  371 bits (952), Expect = e-107
 Identities = 228/672 (33%), Positives = 345/672 (51%), Gaps = 43/672 (6%)

Query: 56  VPVFVISDDSS--RIQADLMEKIYHIIDLNNQYDEQLYDREIESAAAKYEDGVLPPFFKS 113
           +PV++  +  +   I  D++ +++  I ++    E    R I   A  Y D + PPFF++
Sbjct: 96  IPVYLYGETRTARHIPNDILRELHGFIHMHEDTPE-FVARHIIREAKSYLDNLAPPFFRA 154

Query: 114 LKAYVERGNIQFDCPGHQGGQYFRKHPAGRQLYDFYGENVFRSDICNADVDLGDLLIHEG 173
           L  Y   G+  + CPGH GG  F K P G+  + F+GEN+ R+D+CNA  +LG LL H G
Sbjct: 155 LVDYAYDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCNAVDELGQLLDHTG 214

Query: 174 PAMDAEKHAAKVFNADKTYFVMNGTSTSNNVAVAAAVAPGDLVLFDRNNHKSIYNAALVK 233
           P   +E++AA++FNAD  +FV NGTSTSN +   + VA GD+VL DRN HKS  + A++ 
Sbjct: 215 PVAASERNAARIFNADHLFFVTNGTSTSNKIVWHSCVAAGDIVLVDRNCHKSNLH-AIIM 273

Query: 234 DGGRPVYLETSRDPYGFIGGIYARDFDEDYIRKQAA----KVDPVKAKQKRPFRLAIIQL 289
            G  PV+L  +R+ YG IG I   +F  D I+K+        + ++ +  R  R+  +  
Sbjct: 274 TGAIPVFLMPTRNHYGIIGPIPKSEFQPDTIKKKILANPFAREMLEQRPNRKPRILTLTQ 333

Query: 290 GTYDGTIYNAKQVVEKIGHLCDYILFDSAWVGYEQFIPMMRDSSPLLLDLGP-----EDP 344
            TYDG +YN +++   +    D + FD AW+ +  F    RD       +G      ED 
Sbjct: 334 STYDGILYNVEEIKGLLDGEVDTLHFDEAWLPHACFHDFYRDFHA----IGEGRPRCEDS 389

Query: 345 GILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYIDHKRFNNAYNQYASTSPFYPLFATL 404
            +  TQSTHK  AG SQASQI  +D     Q R +D   FN AY  + STSP Y + A+ 
Sbjct: 390 LVFSTQSTHKLLAGISQASQILVQDP----QNRQLDTAWFNEAYLMHTSTSPQYSIIASC 445

Query: 405 DVNAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFVPPVVHGKNW-------EDA 457
           DV A M E   G+ L  ++LV ++  R+ + K             +G++W       +D 
Sbjct: 446 DVAAAMMEQPGGQSLVEESLVEAMEFRRAMRK---------VDEEYGRDWWFSVWGPDDL 496

Query: 458 DTEKIVDDIDYWRFEKGAKWHGFDGYEDNQYFVDPNKFLLTTPGINVQTGEYEDFGIPAT 517
             + I D  D W      +WHGF G ED    +DP K  + TPG++V  G +E+ GIPA 
Sbjct: 497 SDDGICDQTD-WTLRPDERWHGFAGIEDGFNMLDPIKATVLTPGLDVD-GSFEEMGIPAA 554

Query: 518 ILANYLREHGIIPEKNDLNSILFLMTPAETPAKMNNLVSQIVKFESLVKADAPLEDVLPR 577
           I+  YL EHG++ EK  L S   + T   T  + N L+S + +F+     + PL  V+P 
Sbjct: 555 IVTKYLTEHGVVVEKTGLYSFFIMFTIGITKGRWNTLISLLQQFKDDFDKNQPLWRVMPE 614

Query: 578 LYAQNKDRYNGYTIKQLCQELHNFYKGNNAKEYQKEMFLADYFPEQKMTPFDANVELLHN 637
             A+   +Y+   ++ LCQ +H  Y  ++      +++L+D   E  M P DA  ++ H 
Sbjct: 615 FVAK-YPQYDRVGLQDLCQRIHGLYTKHDVARLTTDIYLSDM--EPAMRPADAFAKMAHR 671

Query: 638 NAKLVKLSDIGGETALEGALPYPPGIFCVAPGEKWTKVAQTYFMILEEGINRFPGFAPEI 697
             + V +  + G        PYPPGI  + PGE++ K    Y    +      PGF  ++
Sbjct: 672 EIERVPVDQLEGRVTAVLLTPYPPGIPLLIPGERFNKTIVDYLRFAQAFNRELPGFETDV 731

Query: 698 QG-VYFEQEDGK 708
            G V  E +D K
Sbjct: 732 HGLVAVEVQDRK 743


Lambda     K      H
   0.318    0.137    0.409 

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: 1250
Number of extensions: 56
Number of successful extensions: 9
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: 721
Length of database: 752
Length adjustment: 40
Effective length of query: 681
Effective length of database: 712
Effective search space:   484872
Effective search space used:   484872
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: 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