Alignments for a candidate for acnD in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Echvi_4039 Echvi_4039 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Cola:Echvi_4039
          Length = 925

 Score =  687 bits (1774), Expect = 0.0
 Identities = 373/897 (41%), Positives = 537/897 (59%), Gaps = 75/897 (8%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLTASLKQII----ESKQELDFPWFPARVVCHDILGQTAL 92
           +LP++ R+L EN +R  +   +T    + +        + D P+ PARV+  D  G  A+
Sbjct: 36  ELPFSIRILLENALRNYDDFAITKEHTETLLNWKPEASDKDVPYKPARVLMQDFTGVPAV 95

Query: 93  VDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDR 152
           VD+A LR     KG DP ++NP++P  L+VDHS+ V+Y G +  ++ KN  +E  RN +R
Sbjct: 96  VDIASLRAEAVRKGKDPQKINPLIPVDLVVDHSVQVDYFGTNY-SYKKNVDVEYERNGER 154

Query: 153 FHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHVDA 212
           + F+ W QK+F N  V+P G GI HQ+NLE ++  +  R+G  FPDTLVGTDSHTP V+ 
Sbjct: 155 YEFLKWAQKSFDNFSVVPPGMGICHQVNLEYLAKGVIERDGNVFPDTLVGTDSHTPMVNG 214

Query: 213 LGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKV 272
           +GV+  GVGG+EAE+ +LG+  Y  +P ++G++LTG+   G TATD+VL +TE LR   V
Sbjct: 215 IGVVGWGVGGIEAEAALLGQPIYFIMPQVVGLKLTGELPLGTTATDMVLTITELLRKHGV 274

Query: 273 VSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLV 332
           V  ++E FG G + LT+ DRATISNM+PEFG T   F ID +TLDY++ T R  +Q+KLV
Sbjct: 275 VGKFVEVFGPGLDTLTVPDRATISNMSPEFGCTVTYFPIDDRTLDYMSKTNRSKDQIKLV 334

Query: 333 ETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNP-------------------- 372
           E YAK   LW +D +   Y   +  DL +V  T++GP  P                    
Sbjct: 335 EDYAKANMLWREDEESVKYSSLVELDLGTVEPTVSGPKRPQDKILVRNFKEKFGELLEEV 394

Query: 373 HAR--VPTS--------------------------ELAARGISG------EVENEPGLMP 398
           H R  +P                            E+A +  +G      ++ NE   + 
Sbjct: 395 HGREYIPIDKRDKSRWFSEGGGQPVDKPGDLPEDVEIATKTKNGLKTVEVKINNEEFALS 454

Query: 399 DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEA 458
           DG+++IAAITSCTNTSNP  +I AGL+A+ A  +GL  KPWVKTSLAPGSK V  YLE +
Sbjct: 455 DGSIVIAAITSCTNTSNPSVMIGAGLVAQKARERGLDVKPWVKTSLAPGSKVVTDYLEAS 514

Query: 459 NLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPY 518
            LL +LE+L F +VG+ CT+C G SG L   I   V + DL   +VLSGNRNF+ R+HP 
Sbjct: 515 GLLDDLEALRFHVVGYGCTSCIGNSGPLPKHIAHAVEENDLVVASVLSGNRNFEARVHPQ 574

Query: 519 AKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVK 578
            K  +L SP LVVAYA+AG +  D+ ++ LG D + +PV L +IWPS+ EI  V+   + 
Sbjct: 575 VKMNYLMSPMLVVAYALAGRVDVDLNEEPLGFDPNLEPVYLKDIWPSNDEIFEVMGKVLS 634

Query: 579 PEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEGALAGE----RTLKG 631
           P  F K Y  +F+ +  + +  +P   +Y+W  +STYI+  P+++G L+ E    + ++G
Sbjct: 635 PGDFDKNYGEIFEGNEQWKNLQAPSDKVYNWSEKSTYIKEAPFFQG-LSNEVPEPQNIQG 693

Query: 632 MRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATF 691
            R L  LGD+ITTDH+SP+ A    S AG+YL   G+ ++DFNSY + RG+     R TF
Sbjct: 694 ARVLLKLGDSITTDHISPAGAFAESSPAGQYLVGRGVEKKDFNSYGSRRGNDEVMVRGTF 753

Query: 692 ANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSS 751
           AN ++KN++A      ++G      P G    ++EA E Y     PL+++AG +YG GSS
Sbjct: 754 ANVRIKNQLA-----SREGGYTTHIPSGEEMTVFEASEKYQKDDTPLVVLAGKEYGSGSS 808

Query: 752 RDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG 811
           RDWAAKG  L G+ A++AE +ERIHR+NLVGMGVLPL+F  G++ ++ G+DG E   + G
Sbjct: 809 RDWAAKGTTLLGIHAVIAESYERIHRSNLVGMGVLPLQFAEGQSASSLGLDGKEEITIEG 868

Query: 812 ---SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865
               + P  +L     +  G  V   V CRLD+  E++ Y+ GG+L    ++FL+ +
Sbjct: 869 ITEGLTPLKNLKATAKKDGGAVVNFDVVCRLDSEVEIAYYKNGGILHYVLREFLKQD 925


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: 1978
Number of extensions: 94
Number of successful extensions: 8
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: 925
Length adjustment: 43
Effective length of query: 824
Effective length of database: 882
Effective search space:   726768
Effective search space used:   726768
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