Alignments for a candidate for acnD in Polaribacter dokdonensis DSW-5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Polaribacter dokdonensis DSW-5

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_053974641.1 I602_RS10500 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001280865.1:WP_053974641.1
          Length = 755

 Score =  195 bits (496), Expect = 7e-54
 Identities = 222/803 (27%), Positives = 339/803 (42%), Gaps = 114/803 (14%)

Query: 63  KQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIV 122
           K++   K  +DF   P R+ C D   Q AL+       A  A           VPT +  
Sbjct: 48  KELQRGKDYVDFA--PDRIACQDATAQMALLQFMQAGKAKVA-----------VPTTVHC 94

Query: 123 DHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLE 182
           DH +  + G       AK+    +  + + F+F+      +  I     G GI+HQ+ LE
Sbjct: 95  DHLIQAKEGA------AKDLKHANNTSSEVFNFLESVSNKY-GIGFWKPGAGIIHQVVLE 147

Query: 183 RMSPVIHARNGVAFPD-TLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDI 241
                       AFP   ++GTDSHT +   LG++AIGVGG +A  VM G A  ++ P +
Sbjct: 148 NY----------AFPGGMMIGTDSHTVNAGGLGMVAIGVGGADAVDVMAGMAWELKFPKL 197

Query: 242 IGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPE 301
           IGV+LTGK        D++L + E L  +    + +E+FG GA +++   + TI NM  E
Sbjct: 198 IGVKLTGKLSGWTAPKDVILKVAEILTVKGGTGAIVEYFGPGATSMSCTGKGTICNMGAE 257

Query: 302 FGATAAMFYIDQQTLDYLTLTGRE--AEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDL 359
            GAT + F  D+    YL  T RE  A     ++ Y  TA     +  +  + + +  +L
Sbjct: 258 IGATTSTFGYDESMERYLKATDREDVANAANEIKEYL-TADAEVYENPEQYFDQVIEINL 316

Query: 360 SSVVRTIAGPSNPHARVPT-SELAARGISGE--VENEPGLMPDGAVIIAAITSCTNTSNP 416
           S +   + GP  P       SE+  +  + +  +  E GL          I SCTN+S  
Sbjct: 317 SELGPLLNGPFTPDLSTTVGSEMTEKANANDWPLTVEWGL----------IGSCTNSSY- 365

Query: 417 RNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFAC 476
            ++  A  +A+ A  KGL  K   +  + PGS+ V+   E   +L   E+L   I   AC
Sbjct: 366 EDLSRASSIAQQAIDKGLKTK--AEFGINPGSEQVRYTAERDGILQIFENLDAKIFTNAC 423

Query: 477 TTCNGM-SGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAK-QAFLASPPLVVAYA 534
             C G  +   DP    +        + V S NRNF  R        AF+ASP +  A A
Sbjct: 424 GPCIGQWARYSDPKNAPK-------NSIVHSFNRNFAKRADGNPNTHAFVASPEITAAIA 476

Query: 535 IAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSV 594
           IAG + F+  KD L +++DG+ V            D      + P+ F +V E  +    
Sbjct: 477 IAGRLDFNPLKDKL-INEDGEEVM----------FDEPTGWELPPKGF-EVKENGYLAPD 524

Query: 595 DYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIM 654
           + G  V    +   +   +  P    G+     T+ G + L       TTDH+       
Sbjct: 525 EDGSGVVVSVNDDSERLQLLTPFTPLGS-----TITGAKLLIKAFGKCTTDHI------- 572

Query: 655 MDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLAR 714
             S AG +L   G  +   N+      +    ++  F   +L  E   V    ++     
Sbjct: 573 --SMAGPWLRFRGHLDNIANNTLIGAVNAFN-KKTNFVKNQLTGEYDAVPAVQRE----- 624

Query: 715 IEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 774
            + EGI T                I++   +YG+GSSR+ AA   R  GV A++ + F R
Sbjct: 625 YKKEGIKT----------------IVVGDHNYGEGSSREHAAMQPRHLGVAAVIVKSFAR 668

Query: 775 IHRTNLVGMGVLPLEFKAGENRATYGI---DGTEVFDVIGSIAPRADLTVIITRKNGERV 831
           IH TNL   G+L L F    N A Y +   D T  F  +   AP   LT+ I  K+G   
Sbjct: 669 IHETNLKKQGMLGLTF---ANEADYDLIQEDDTFNFTDLNEFAPDKQLTLEIVHKDGSSD 725

Query: 832 EVPVTCRLDTAEEVSIYEAGGVL 854
            + +    + A ++  Y  G  L
Sbjct: 726 TIKLNHTYNKA-QIDWYNEGSAL 747


Lambda     K      H
   0.318    0.136    0.397 

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: 1493
Number of extensions: 75
Number of successful extensions: 4
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: 867
Length of database: 755
Length adjustment: 41
Effective length of query: 826
Effective length of database: 714
Effective search space:   589764
Effective search space used:   589764
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.

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Protein sequences (fasta format)
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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
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