GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adiA in Shewanella amazonensis SB2B

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 6939240 Sama_3334 ornithine decarboxylase (RefSeq)

Query= BRENDA::P28629
         (755 letters)



>lcl|FitnessBrowser__SB2B:6939240 Sama_3334 ornithine decarboxylase
           (RefSeq)
          Length = 720

 Score =  324 bits (831), Expect = 9e-93
 Identities = 208/675 (30%), Positives = 326/675 (48%), Gaps = 30/675 (4%)

Query: 75  LIGKLHERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRY 134
           ++ K+     N+P+F+    E+A      D  + +     +     DF   +   A+ RY
Sbjct: 47  IVDKIKNTGLNLPIFVSVCCEEAFPD---DFCDTITGVFELCNAKTDFYGKQVETAVRRY 103

Query: 135 RQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIER 194
           ++ LLPP F  L KY ++   ++A PGHQGG  F K P GR + D++GE +FR+DM    
Sbjct: 104 QESLLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETVFRSDMCNAD 163

Query: 195 TSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNC 254
             LG LL H GA  +++ YAA+V+ AD+++ V+ GTS SN+ +  A +   D+V+ DRN 
Sbjct: 164 VKLGDLLIHEGAPHDAQAYAAKVYNADKTYFVLNGTSASNKVVCNALLAPGDLVLFDRNN 223

Query: 255 HKSIEQG-LMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKP 313
           HKS   G L+  GA PVY+  +RN +G IG I         L+ +I +    + +A +  
Sbjct: 224 HKSNHHGALIQAGATPVYLETARNPFGFIGGIDSHCFDEAYLRDEIGKVAPERVQAARPF 283

Query: 314 SYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDH 373
              ++   TYDG  YNA++  D +    D + FD AW GY +F P+  D   +  E G  
Sbjct: 284 RLAIIQLGTYDGTIYNARQVVDRIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELGAE 343

Query: 374 NGPTVFATHSTHKLLNALSQASYIHVREG-----RGAINFSRFNQAYMMHATTSPLYAIC 428
           + P +  T S HK     SQ S IH ++          N  RFN A+MMHA+TSP Y + 
Sbjct: 344 D-PGIIVTQSVHKQQAGFSQTSQIHKKDSHIKGQERYCNHKRFNNAFMMHASTSPFYPLF 402

Query: 429 ASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVTDPQ 488
           A+ DV   M +G SG  L +E +   ++ R+ + +  K        + KP+       P 
Sbjct: 403 AALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCK--------YIKPF------IPT 448

Query: 489 TGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGM-GEDG 547
           T +   +    T+ +      +   PG  WH F         +DP K  +  PG+  E G
Sbjct: 449 TVEGEPWQSFDTERMADDLRFFEFEPGLKWHAFDGYEKGQYFVDPCKFLLTTPGINAETG 508

Query: 548 ELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRHYDA 607
           E E+ G+PA ++  +L  + I+P +     I+FL +      K   LV  +  F++  D 
Sbjct: 509 EYEDFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDMAKMQHLVTQIARFEKLIDE 568

Query: 608 NTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAY--SGLPVAEVTP 665
           + PL++V+P +     + Y    I  L   M       N      E +  +  P A + P
Sbjct: 569 DAPLSEVLPNVYRTNRERYEGYSIRRLCQEMHDLYVSRNVKQLQKEMFRAAHFPKAVMNP 628

Query: 666 REAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLRSLQ 725
           ++A  A V    ELV +  + G+IAA   +PYPPG+  ++ GE +G        Y  +L+
Sbjct: 629 QDANIAFVRGKAELVPLSEIEGQIAAEGALPYPPGVLCMVPGEVWG---GAVQRYFLALE 685

Query: 726 SWDHHFPGFEHETEG 740
              +  PGF  E +G
Sbjct: 686 EGINLLPGFAPELQG 700


Lambda     K      H
   0.319    0.135    0.414 

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: 1262
Number of extensions: 65
Number of successful extensions: 7
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: 755
Length of database: 720
Length adjustment: 40
Effective length of query: 715
Effective length of database: 680
Effective search space:   486200
Effective search space used:   486200
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: 55 (25.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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