GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS16405 CA265_RS16405 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Pedo557:CA265_RS16405
          Length = 759

 Score =  212 bits (539), Expect = 8e-59
 Identities = 229/806 (28%), Positives = 345/806 (42%), Gaps = 123/806 (15%)

Query: 65  KRDLDFPWF-PARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDHSLA 123
           KR  D+  F P RV   D   Q AL+           Q G P      VP  +  DH + 
Sbjct: 51  KRGSDYVDFAPDRVAMQDATAQMALLQFM--------QAGRP---QVAVPSTVHCDHLIT 99

Query: 124 VECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKMSPV 183
            + G       AK  + E       F F+      +  +    PG GI+HQ+ LE     
Sbjct: 100 AKEGAAIDLPHAKTESAEV------FDFLSSVSNKY-GIGFWKPGAGIIHQVVLENY--- 149

Query: 184 IHADNGVAYPD-TCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGVEL 242
                  A+P    +GTDSHT +   LG++AIGVGG +A +VM G    ++ P ++GV+L
Sbjct: 150 -------AFPGGMMIGTDSHTVNAGGLGMVAIGVGGADACDVMAGLPWELKFPKLIGVKL 202

Query: 243 TGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGATA 302
           TGK      A D++L +   L  +   GA +E+ G+GA+S++   + TI NM  E GAT 
Sbjct: 203 TGKLNGWTAAKDVILKVAGILTVKGGTGAIVEYFGDGATSMSCTGKGTICNMGAEIGATT 262

Query: 303 AMFFIDEQTIDYLRLTGR---TDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVV 359
           + F  DE    YLR TGR    DE  K+       A ++AD      +++V++ DL ++ 
Sbjct: 263 STFGYDESMERYLRATGRNEVADEANKIAAYLTGDAEVYAD--PENYFDQVIEIDLDTLE 320

Query: 360 RNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRN 419
             + GP  P    P S +               EAE       V    I SCTN+S   +
Sbjct: 321 PYLNGPFTPDLATPVSQM-------------KVEAEKNGWPLKVEWGLIGSCTNSSY-ED 366

Query: 420 VIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTT 479
           +  AA +A  A A+GL  K      + PGS+ V    +    L   E L   I   AC  
Sbjct: 367 LSRAASIANQAIAKGLVTK--ADFGINPGSEQVRYTADRDGFLKTFEDLNATIFTNACGP 424

Query: 480 CNGMSGALDPKIQQEIIDRDLYATAVLSGNRNF----DGRIHPYAKQAFLASPPLVVAYA 535
           C GM      +  ++        T V S NRNF    DG  + +   AF+ASP +V A A
Sbjct: 425 CIGMWDRTGAEKAEK-------NTIVHSFNRNFAKRADGNPNTF---AFVASPEMVAAIA 474

Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA 595
           I+G + F+   D L T+  G+ V L    P+  E+         P +   V +  +   A
Sbjct: 475 ISGNLGFNPLTDTL-TNDKGEQVKLDP--PTGFEL---------PTKGFAVEDAGYQAPA 522

Query: 596 ASGESVSPLYDWRPQSTYIRRP-PYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAI 654
           A G SV  L         +  P   WEG       L+ L+ L       TTDH+      
Sbjct: 523 ADGSSVQVLVSPTSHRLQLLDPFTPWEGT-----DLQGLKLLIKAKGKCTTDHI------ 571

Query: 655 MLNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLA 714
              S AG +L         F  +  +  +++      + N    N    + G+   G + 
Sbjct: 572 ---SMAGPWL--------KFRGHLDNISNNMLIGAVNYFNDKTDNVKNELTGEY--GPVP 618

Query: 715 RIEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFE 774
             + + K   +              I++   +YG+GSSR+ AA   R  GV  ++ + F 
Sbjct: 619 ATQRDYKAAGLGS------------IVVGDENYGEGSSREHAAMEPRHLGVRAVLVKSFA 666

Query: 775 RIHRTNLIGMGVLPLEF--KPGVNRLTLGLDGTETYDVIG--ERQPRATLTLVVNRKNGE 830
           RIH TNL   G+L L F  K   +++       +T D++G  E  P   LTLV++  +G 
Sbjct: 667 RIHETNLKKQGMLGLTFADKDDYDKIL----EDDTIDILGLTEFTPDQPLTLVLHHADGT 722

Query: 831 RVEVPVTCRLDSDEEVSIYEAGGVLH 856
           +   PV    ++ +++  ++AGG L+
Sbjct: 723 QESFPVNHSYNA-QQIDWFKAGGALN 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: 1576
Number of extensions: 88
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 869
Length of database: 759
Length adjustment: 41
Effective length of query: 828
Effective length of database: 718
Effective search space:   594504
Effective search space used:   594504
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