GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6939240
          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 (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