GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3608667 Dshi_2060 aconitate hydratase 2
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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