Alignments for a candidate for acn in Algoriphagus aquaeductus T4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Algoriphagus aquaeductus T4

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_111391081.1 CLV31_RS01395 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>NCBI__GCF_003253485.1:WP_111391081.1
          Length = 753

 Score =  209 bits (531), Expect = 6e-58
 Identities = 235/838 (28%), Positives = 356/838 (42%), Gaps = 151/838 (18%)

Query: 51  PATLTDSLL----------QLVGR-KRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA 99
           P TLT+ +L          Q  GR K  +DF   P RV   D   Q AL+          
Sbjct: 29  PLTLTEKILYAHLTEGPASQAYGRGKSYVDFQ--PDRVAMQDATAQMALLQFM------- 79

Query: 100 DQGGDPAKVNPVVPVQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAF 159
            Q G   +    VP  +  DH +  E G       AK++      N + + F+      +
Sbjct: 80  -QAG---REKVAVPSTVHCDHLIQAEVGAEKDLNKAKDK------NREVYDFLASVSNKY 129

Query: 160 KNVDVIPPGNGIMHQINLEKMSPVIHADNGVAYPD-TCVGTDSHTPHVDALGVIAIGVGG 218
             +    PG GI+HQ+ LE            A+P    +GTDSHTP+   LG+IAIGVGG
Sbjct: 130 -GIGFWKPGAGIIHQVVLENY----------AFPGGMMIGTDSHTPNAGGLGMIAIGVGG 178

Query: 219 LEAENVMLGRASWMRLPDIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGE 278
            +A +VM G    ++ P ++GV+LTGK     +A D++L +   L  +   GA +E+ GE
Sbjct: 179 ADACDVMAGLPWELKFPKLIGVKLTGKMSGWTSAKDVILKVAGILTVKGGTGAIVEYFGE 238

Query: 279 GASSLTLGDRATISNMAPEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLW 338
           GA SL+   + TI NM  E GAT ++F  DE++  YL+ TGR D         A  A   
Sbjct: 239 GARSLSATGKGTICNMGAEIGATTSIFGYDEKSAAYLQGTGRAD--------IAAMADAI 290

Query: 339 ADSLKNAE---------YERVLKFDLSSVVRNMAGPSNPHKRLPTS----ALAERGIAVD 385
           A+ L   E         ++++++ +LS +  ++ GP  P    P S    A+ E G    
Sbjct: 291 AEHLTGDEEVYANPEQYFDQLIEINLSELEPHVNGPFTPDLAWPISKFAAAVKENGWPAK 350

Query: 386 LDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLARKPWVKSSL 445
           LD                 +  I SCTN+S   ++  AA LA+ A  + L  K   + ++
Sbjct: 351 LD-----------------VGLIGSCTNSSY-EDISRAASLAQQAVDKKLNAKS--EYTI 390

Query: 446 APGSKAVELYLEEANLLPDLEKLGFGIVAFACTTCNGMSGALDPKIQQEIIDRDLYATAV 505
            PGS+ V   +E    L    K+G  ++A AC  C G       + Q++        + +
Sbjct: 391 TPGSEQVRFTVERDGFLDTFGKMGGVVLANACGPCIGQWARHGAEKQEK-------NSII 443

Query: 506 LSGNRNFDGRIHPYAK-QAFLASPPLVVAYAIAGTIRFDIEKDVLGTDQDGKPVYLKDIW 564
            S NRNF  R        AF+ASP +V A AIAG + F+   D L T+ +G+ V L +  
Sbjct: 444 TSFNRNFAKRADGNPNTHAFVASPEIVTALAIAGDLTFNPLTDTL-TNAEGQQVKLDE-- 500

Query: 565 PSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGESVSPLYDWRPQSTYIR---RPPYWE 621
           P   E+         P +   V +  +   A  G SV  L    P S  ++     P WE
Sbjct: 501 PRGLEL---------PTKGFAVEDAGYQAPAEDGSSVQVLVS--PTSDRLQLLDSFPAWE 549

Query: 622 GALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAAGEYLARMGLPEEDFNSYATHR 681
           G       L  L+ L       TTDH+         S AG +L   G             
Sbjct: 550 GT-----DLTGLKLLIKAKGKCTTDHI---------SMAGPWLKYRG------------- 582

Query: 682 GDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEGKVVRMWEAIETYMDRKQPLII 741
             HL       +N  LI  +   +         + +  G+   +      Y       I+
Sbjct: 583 --HLD----NISNNMLIGAVNAFNDATNS---VKNQLTGEYGEVPATQRQYKAAGIGSIV 633

Query: 742 IAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLIGMGVLPLEF-KPGVNRLTL 800
           +   +YG+GSSR+ AA   R  GV  I+ + F RIH TNL   G+L L F  P    L  
Sbjct: 634 VGDENYGEGSSREHAAMEPRFLGVRAILVKSFARIHETNLKKQGMLALTFANPSDYDL-- 691

Query: 801 GLDGTETYDVIG--ERQPRATLTLVVNRKNGERVEVPVTCRLDSDEEVSIYEAGGVLH 856
            +   ++ D++G     P   L +V+N ++G    +       ++ ++  ++AG  L+
Sbjct: 692 -IQENDSIDIVGLTSFAPGKPLQIVLNHQDGSSHSIQAN-HTYNEGQIEWFKAGSALN 747


Lambda     K      H
   0.318    0.135    0.398 

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: 1502
Number of extensions: 82
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 869
Length of database: 753
Length adjustment: 41
Effective length of query: 828
Effective length of database: 712
Effective search space:   589536
Effective search space used:   589536
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.

Downloads

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

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:

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
the source code
instructions for running GapMind on your computer

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