GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Marinobacter adhaerens HP15

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate GFF3491 HP15_3433 aconitate hydratase 1

Query= SwissProt::P37032
         (891 letters)



>FitnessBrowser__Marino:GFF3491
          Length = 919

 Score = 1204 bits (3116), Expect = 0.0
 Identities = 602/913 (65%), Positives = 717/913 (78%), Gaps = 29/913 (3%)

Query: 3   VGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTT 62
           + +DSL+T S L   GKT++YYSL +A +     +NRLP+SLKVL+ENLLR EDG TV  
Sbjct: 6   LSKDSLNTLSSLDAGGKTFHYYSLPKAADT-LGDLNRLPFSLKVLMENLLRNEDGTTVDR 64

Query: 63  KDIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPL 122
             I A+  W+ ++ S  EI FRP RVLMQDFTGVP VVDLAAMR A+   G +   I+PL
Sbjct: 65  SHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPL 124

Query: 123 SPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGIC 182
           SPVDLVIDHSVMVDKF  A + + N  IE+ERN+ERYEFLRWGQ+AF NF+VVPPGTGIC
Sbjct: 125 SPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGIC 184

Query: 183 HQVNLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242
           HQVNLEYLGKTVW  + DG+  AYPDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQ
Sbjct: 185 HQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQ 244

Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302
           PVSMLIPEV+GFK++GKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYG GL D+P+ADR
Sbjct: 245 PVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADR 304

Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362
           ATI+NMAPEYGATCGFFPVD++TIKY+ LTGR++  + LVEAYAKAQG+W +  +E PV+
Sbjct: 305 ATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE-PVY 363

Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNK---- 418
           TD+L LD+G VE SLAGPKRPQD+V L ++   F   L+E  +   + +   ++++    
Sbjct: 364 TDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFE-LLMETAEGPAENREANLESEGGQT 422

Query: 419 ----DFQMKH-----------------GHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEK 457
               D   KH                 G VVIAAITSCTNTSNPSV+MAAGL+A+KA++K
Sbjct: 423 AVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQK 482

Query: 458 GLQRKPWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISH 517
           GL  KPWVK+SLAPGSKVVTDYL+  G Q  LD+LGFNLVGYGCTTCIGNSGPLPD +  
Sbjct: 483 GLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEK 542

Query: 518 CVAEHDLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDK 577
            +++ DL V+SVLSGNRNFEGRVHP V+ NWLASPPLVVAYAL G    DLS++P+G DK
Sbjct: 543 AISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDK 602

Query: 578 EGNDVYLKDIWPSNEEIAAEVAKVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDS 637
           +GN VYLKD+WPS +EIA  V KV   MFRKEYAEVF GDA W++I+    + YEW+  S
Sbjct: 603 DGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKS 662

Query: 638 TYIQHPPFFENLSLKPEPLKPIKQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKG 697
           TYIQHPPFFE L  +P+ +  IK A +LAL GDS+TTDHISPAGS K  +PAG YL+  G
Sbjct: 663 TYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHG 722

Query: 698 VDEKDFNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRY 757
           V+ KDFNSYGSRRGNHEVMMRGTFAN+RIRNEM  G EGG T++VPTGE M+IYDAAM+Y
Sbjct: 723 VEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKY 782

Query: 758 QENQQDLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFK 817
           QE    LV+IAGKEYGTGSSRDWAAKGT LLGVKAV+ ES+ERIHRSNLIGMG++PLQF 
Sbjct: 783 QEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFP 842

Query: 818 EGTTRKTLKLDGSERISIE-ISDKLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYY 876
           EGT RK+LKL G E ISIE +S ++ PG  + +T++ +DG  E  E   RIDTA+E  Y+
Sbjct: 843 EGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYF 902

Query: 877 KNGGILQYVLRKI 889
           K+GGIL YV+R++
Sbjct: 903 KHGGILHYVVREM 915


Lambda     K      H
   0.316    0.134    0.393 

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: 2253
Number of extensions: 99
Number of successful extensions: 6
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: 891
Length of database: 919
Length adjustment: 43
Effective length of query: 848
Effective length of database: 876
Effective search space:   742848
Effective search space used:   742848
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 (21.6 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