Alignments for a candidate for acnD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Escherichia coli BW25113

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 15396 b1276 aconitate hydratase (NCBI)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Keio:15396
          Length = 891

 Score =  716 bits (1847), Expect = 0.0
 Identities = 393/897 (43%), Positives = 551/897 (61%), Gaps = 40/897 (4%)

Query: 1   MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT- 59
           MS+ +    +  L      Y      + A + G   +LP + +VL ENL+R  +   +T 
Sbjct: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE 60

Query: 60  ----ASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPV 115
               A    +  +  + +  + PARV+  D  G  A+VDLA +R+A+   GGD A+VNP+
Sbjct: 61  EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120

Query: 116 VPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGI 175
            P  L++DHS+ V+  G D +AF +N  +E  RN +R+ F+ W ++AF    V+P G GI
Sbjct: 121 SPVDLVIDHSVTVDRFG-DDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGI 179

Query: 176 MHQINLERMSPVIHAR----NGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLG 231
            HQ+NLE +   + +       +A+PDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG
Sbjct: 180 CHQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLG 239

Query: 232 RASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGD 291
           +   M +PD++G +LTGK + GITATD+VL +T+ LR   VV  ++EF+G+G ++L L D
Sbjct: 240 QPVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLAD 299

Query: 292 RATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVY 351
           RATI+NM+PE+GAT   F ID  TLDY+ L+GR  +QV+LVE YAK  G+W +   + ++
Sbjct: 300 RATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIF 359

Query: 352 PRTLHFDLSSVVRTIAGPSNPHARVPTSELA-ARGISGEVE----------------NEP 394
             TL  D++ V  ++AGP  P  RV   ++  A   S E+E                   
Sbjct: 360 TSTLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQ 419

Query: 395 GLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLY 454
             +PDGAV+IAAITSCTNTSNP  ++AAGLLA+ A   GL R+PWVK SLAPGSK V  Y
Sbjct: 420 YQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDY 479

Query: 455 LEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGR 514
           L +A L P L+ LGF +VG+ CTTC G SG L   I+  +   DL   AVLSGNRNF+GR
Sbjct: 480 LAKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGR 539

Query: 515 IHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIA 574
           IHP  K  +LASPPLVVAYA+AG +  ++  + +G D+ G PV L +IWPS  EI A   
Sbjct: 540 IHPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEI-ARAV 598

Query: 575 ASVKPEQFRKVYEPMFDLSVDY-GDKV--SPLYDWRPQSTYIRRPPYW---EGALAGERT 628
             V  E FRK Y  +F+ + ++ G  V  S  Y W+  STYIR  P++   +   A    
Sbjct: 599 EQVSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVED 658

Query: 629 LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQR 688
           + G R LA+LGD++TTDH+SP+ +I  DS AG YL   G+  +DFNSY + RG+H    R
Sbjct: 659 IHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMR 718

Query: 689 ATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQ 748
            TFAN +++NEM  V G   +G + R  P+  V  +++A   Y   + PL +IAG +YG 
Sbjct: 719 GTFANIRIRNEM--VPG--VEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGS 774

Query: 749 GSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFD 808
           GSSRDWAAKG RL G+  ++AE FERIHR+NL+GMG+LPLEF  G  R T G+ G E  D
Sbjct: 775 GSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKID 834

Query: 809 V--IGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863
           +  + ++ P A + V +TR +G +  VP  CR+DTA E++ Y+  G+L    ++ L+
Sbjct: 835 IGDLQNLQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNMLK 891


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: 1924
Number of extensions: 95
Number of successful extensions: 9
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: 867
Length of database: 891
Length adjustment: 43
Effective length of query: 824
Effective length of database: 848
Effective search space:   698752
Effective search space used:   698752
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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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
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