GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Dinoroseobacter shibae DFL-12

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 3608667 Dshi_2060 aconitate hydratase 2 (RefSeq)

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__Dino:3608667
          Length = 930

 Score =  325 bits (834), Expect = 6e-93
 Identities = 285/932 (30%), Positives = 431/932 (46%), Gaps = 125/932 (13%)

Query: 5   YRKHVAERAAEGIAPKPLD-ANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAYV 63
           Y + +A R  +G+ PKP+D A   + ++  +K+P        L        PG   AA  
Sbjct: 7   YLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGTTSAAGA 66

Query: 64  KAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKALSH 121
           KA FL  I  GE+    +TP+ A ELL  M+GG ++  L+D    DDA LA  AA+ L  
Sbjct: 67  KAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQAAEVLKT 126

Query: 122 TLLMFDNFYDVEEKA-KAGNEYAKQVMQSWADAEWFLNRPALAEKL-TVTVFKVTGETNT 179
            + +++   D  + A +AGN  A  ++QS+A AE+F   P + +++  VT     G+ +T
Sbjct: 127 QVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAAEGDIST 186

Query: 180 DDLSPAPDAWSRPDIPLHALAMLKNAR----EGIEPDQPGVVGPIKQIEALQQKGFPLAY 235
           D LSP   A SR D  LH   M+  A     E ++   PG     K++  + +KG     
Sbjct: 187 DLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPG-----KRVMLIAEKG----- 236

Query: 236 VGDVVGTGSSRKSATNSV-LWFMGDDIPHVPNKRGGGLCLGGK-IAPIFFNTMEDAGAL- 292
               +G GSSR S  N+V LW      P+VP      +  G   I+PIF  T+   G + 
Sbjct: 237 ---TMGVGSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIG 293

Query: 293 -----------------------PIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFE 329
                                  PI     +++ G V+ +     ++ + + GE LA   
Sbjct: 294 IDLKNWVKKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVS 353

Query: 330 LK-TDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKM 388
              +   ++ ++AGG   ++ G+ L T A E LG+  + VF  AK+++   +G +  +K+
Sbjct: 354 SAFSPQAVEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKI 413

Query: 389 VGRACGVKGIRPGAYCEP------KMTSVGSQDTTGPMTRDELKDLAC--LGFSADLVMQ 440
                  +G+ PG           ++  VGSQDTTG MT  EL+ +A   L  + D   Q
Sbjct: 414 FN--ANARGVTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQ 471

Query: 441 SFCHTAA-YPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIHSW-------LNRMLLPD-T 491
           S CHTA+ +      NT   +  F+   G ++ R   GV HS        LN + + D  
Sbjct: 472 SGCHTASVWDLKAQANTPRLMA-FMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWD 530

Query: 492 VGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVH 551
           +  GGDSHTR   G++F A SG VA A ATG   + +PESV V FKGKM   +  RD+VH
Sbjct: 531 IIIGGDSHTRMSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVH 590

Query: 552 AIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKL 611
           A     + Q           N+F GR++E+  +  L  +QAF  TD +AE  A       
Sbjct: 591 ATQAQMLAQ--------HGDNVFQGRVIEVH-IGTLLADQAFTFTDWTAEMKAKASICIS 641

Query: 612 NKEPIIEYLNSNIVLLKWMIAEGY-GDRRTLERRIQGMEKWLA-----NPELLEADADAE 665
           N + +IE L      ++ MI +G   D + L   I      +A         L+ D  A 
Sbjct: 642 NDDTLIESLEIAKQRIQVMIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTAR 701

Query: 666 YAAVIDIDLADIKEPILCAPN----------DPDDARPLSAVQGE-KIDEVFIGSCMTNI 714
           Y A + +DL  I EP++  P+            D  RP+S    E KID  F+GSCM + 
Sbjct: 702 YFAEVVVDLDQIVEPMIADPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHK 761

Query: 715 GHFRAAGKL---LDAHKGQLPTR--LWVAPPTRMDAAQLTEEGYYSVFGKSGA------- 762
           G  +   ++   L+   G++  +  L +A PT     +L EEG + V  K          
Sbjct: 762 GDVKIVAQMLRNLEKANGEVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSA 821

Query: 763 -------------RIEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGANV-----F 804
                         +E PGC+LCMGNQ + A G TV++TSTR F  R+   +        
Sbjct: 822 PKEKARTEYENILYLERPGCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESL 881

Query: 805 LASAELAAVAALIGKLPTPEEYQTYVAQVDKT 836
           L S  +  ++A++G+ PT EEY+T V  ++ T
Sbjct: 882 LGSTPVVVLSAILGRTPTVEEYKTAVEGINLT 913


Lambda     K      H
   0.317    0.136    0.400 

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: 1706
Number of extensions: 99
Number of successful extensions: 13
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: 865
Length of database: 930
Length adjustment: 43
Effective length of query: 822
Effective length of database: 887
Effective search space:   729114
Effective search space used:   729114
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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