Aligments for a candidate for acn in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources