GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Chryseobacterium arthrosphaerae CC-VM-7

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_065400933.1 BBI00_RS21750 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_001684965.1:WP_065400933.1
          Length = 927

 Score =  328 bits (842), Expect = 7e-94
 Identities = 285/928 (30%), Positives = 444/928 (47%), Gaps = 114/928 (12%)

Query: 3   EEYRKHVAERAAEGIAPKPLD-ANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAA 61
           ++Y K + ER  +G+ PKP+D A  ++ ++  +K+    +    L        PG   AA
Sbjct: 5   KDYIKEIEERKTQGLHPKPIDSAELLSEIIAQIKDSGNADRTDSLQFFIYNTLPGTTSAA 64

Query: 62  YVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKAL 119
            VKA FL  I  GE+    +TP+ A ELL  M+GG +I  L+D    +D  +A  AA  L
Sbjct: 65  GVKAQFLKEIILGESVVEEITPDFAFELLSHMKGGKSIEVLLDLALGNDTAIAQQAADVL 124

Query: 120 SHTLLMFD-NFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKL-TVTVFKVTGET 177
              + +++ +   +++   +GN  AK++++S+A AE+F   P +AE++  VT     G+ 
Sbjct: 125 KTQVFLYEADTNRLKDAYNSGNAIAKEILESYAKAEFFTKLPEVAEEIKVVTYIAGEGDI 184

Query: 178 NTDDLSPAPDAWSRPDIPLHALAMLK-NAREGIEPDQPGVVGPIKQIEALQQKGFPLAYV 236
           +TD LSP   A SR D  LH   M+   A++ I+  Q     P   +  + +KG      
Sbjct: 185 STDLLSPGNQAHSRSDRELHGKCMITPEAQQEIKALQ--AQHPDASVMLIAEKG------ 236

Query: 237 GDVVGTGSSRKSATNSV-LWFMGDDIPHVPNKRGGGLCLGGK-IAPIFFNTMEDAGALPI 294
              +G GSSR S  N+V LW      P+VP      +  G   I+PIF  T++  G + I
Sbjct: 237 --TMGVGSSRMSGVNNVALWTGKQASPYVPFVNIAPIVGGTNGISPIFLTTVDVTGGIGI 294

Query: 295 EV------------------------DVSNLNMGDVIDVYPYKGEVRNHETGELLATFEL 330
           ++                        +  ++  G V+ +   + ++ N +  EL+   + 
Sbjct: 295 DLKNWVKKVDENGNPVRNEAGEVILEEAYSVATGTVLTINTKEKKLYNGDQ-ELIDLTKS 353

Query: 331 KTDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKMVG 390
            T   ++ ++AGG   ++ G+ L T A + LG+    VF  +K+++   +G +  +K+  
Sbjct: 354 FTPQKMEFIKAGGSYAIVFGKKLQTFAAQTLGIEAPVVFAPSKEISHEGQGLTAVEKIFN 413

Query: 391 R-ACGV---KGIRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFS--ADLVMQSFCH 444
           R A G    K +  G+    K+  VGSQDTTG MT  EL+ +A    S   D   QS CH
Sbjct: 414 RNAVGTTPGKVLHAGSDVRVKVNIVGSQDTTGLMTAQELESMAATVISPTVDGAYQSGCH 473

Query: 445 TAA-YPKPVDVNTHHTLPDFIMNRGGVSLRPGDG-------VIHSWLNRMLLPD-TVGTG 495
           TA+ + K    N    L  F+ + G ++ R   G       VIH  LN + + +  +  G
Sbjct: 474 TASVWDKKAQANIPK-LMKFMNDFGLITARDPKGEYHSMTDVIHKVLNDITVDEWAIIIG 532

Query: 496 GDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPL 555
           GDSHTR   G++F A SG VA A ATG   + +PESV V FKG+M+P +  RD+VHA   
Sbjct: 533 GDSHTRMSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGEMKPHMDFRDVVHATQA 592

Query: 556 YAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEP 615
             +KQ        G +N+F GRI+E+  +  L  +QAF  TD +AE  A           
Sbjct: 593 QMLKQ-------FGGENVFQGRIIEVH-IGTLPADQAFTFTDWTAEMKAKASINISEDNT 644

Query: 616 IIEYLNSNIVLLKWMIAEGYGD-RRTLERRIQGMEKWL-----ANPELLEADADAEYAAV 669
           +IE L      ++ MI +G  +  + L+  I    K +          L  DA+A+Y A 
Sbjct: 645 LIESLEIAKGRIQIMIDKGMDNHNKVLQGLIDKANKRIEEIRSGEKPALTPDANAKYYAE 704

Query: 670 IDIDLADIKEPILCAPN----------DPDDARPLSAVQGE-KIDEVFIGSCMTNIGHFR 718
           + +DL  I EP++  P+            D  R LS   GE K+D  F+GSCM + G  +
Sbjct: 705 VVVDLDVIVEPMIADPDVNNEDVSKRYTHDTIRDLSYYGGEKKVDLGFVGSCMVHKGDLK 764

Query: 719 AAGKLL-----DAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGK-SGAR--------- 763
              ++L        K +    L VA PT     +L  EG + +  K SG           
Sbjct: 765 IVSQMLRNLEKQQGKVEFNAPLVVAAPTYNIIDELKAEGDWELLEKYSGFEFNDNAPKGE 824

Query: 764 ----------IEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGA-----NVFLASA 808
                     +E PGC+LCMGNQ + A G TV++TSTR F  R+   +        LAS 
Sbjct: 825 ARTQYENVMYLERPGCNLCMGNQEKAAKGDTVLATSTRLFQGRVVEDSERKKGESLLAST 884

Query: 809 ELAAVAALIGKLPTPEEYQTYVAQVDKT 836
            +  ++A+IG++P+ +EY+  V  +D T
Sbjct: 885 PVVVLSAIIGRIPSIDEYKAAVEGIDLT 912


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: 1785
Number of extensions: 100
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: 927
Length adjustment: 43
Effective length of query: 822
Effective length of database: 884
Effective search space:   726648
Effective search space used:   726648
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 24 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