GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO353_21605 AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21605
          Length = 866

 Score = 1386 bits (3587), Expect = 0.0
 Identities = 668/856 (78%), Positives = 760/856 (88%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YRKH+ ERAA GI P+PL+A Q A LVELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1   VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKGEA SPL+  ++A+ELLGTMQGGYNI  L+D LD A+LA +AA  L 
Sbjct: 61  AYVKAGFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVDLLDSAELAAVAAAQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAK GN +A+ V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAQGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ GV GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGVTGPMKQIETMRGEGFPIAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+P+VPNKR GG C G KIAPIF+NTMEDAGALPIE DV+N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDVID+YP+ G+V  H + E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MNMGDVIDLYPHAGKVTKHNSDEILTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP SD+F++ +  AES +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPPSDLFKKPEAPAESTKGFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFS DLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSTDLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFKGKM
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPG+TLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGL +L +EQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+KE I EYL+SNI LL+WMI EGYGD RTLERR Q ME W+ANPEL+ A
Sbjct: 601 ERSAAGCTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAMEAWIANPELMVA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYA +I+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLLD  KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARV 
Sbjct: 721 GKLLDQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVE 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
             +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY  Y  ++D  A D 
Sbjct: 781 PNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTMASDV 840

Query: 841 YRYLNFNQLSQYTEKA 856
           YRYL+F+Q++++ E A
Sbjct: 841 YRYLSFDQIAEFREAA 856


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: 2149
Number of extensions: 82
Number of successful extensions: 1
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: 866
Length adjustment: 42
Effective length of query: 823
Effective length of database: 824
Effective search space:   678152
Effective search space used:   678152
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.

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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