GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS16405 CA265_RS16405 aconitate
           hydratase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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