Alignments for a candidate for acnD in Laceyella sediminis RHA1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Laceyella sediminis RHA1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_022736982.1 CLV36_RS07505 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_003003125.1:WP_022736982.1
          Length = 907

 Score =  683 bits (1762), Expect = 0.0
 Identities = 371/872 (42%), Positives = 530/872 (60%), Gaps = 47/872 (5%)

Query: 33  GAYAKLPYTSRVLAENLVRRCEPEMLTAS----LKQIIESKQELDFPWFPARVVCHDILG 88
           G  ++LP++ +VL E  VR+ + + +T      L    + + + +  + PAR+V  D  G
Sbjct: 33  GPVSRLPFSIKVLLEAAVRQYDGKAVTKEHIEQLATWADKRSDKEIAFKPARIVLQDFTG 92

Query: 89  QTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRR 148
             A+VDLA LR A+A  GGDP ++NP++P  L++DHS+ V+  G  +DA   N  +E  R
Sbjct: 93  VPAVVDLAALRSAMARVGGDPERINPLIPVDLVIDHSVMVDKAG-TQDALEYNMNLEFER 151

Query: 149 NEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN----GVAFPDTLVGTD 204
           NE+R+  + W  ++  N   +P   GI+HQ+NLE ++ V   R      V FPD+LVGTD
Sbjct: 152 NEERYRLLRWAAESLDNFRAVPPATGIVHQVNLEYLANVAATREVDGETVVFPDSLVGTD 211

Query: 205 SHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALT 264
           SHT  ++ LGV+  GVGG+EAE+ MLG+  Y   P++IG +LTG+   G TATD+ L +T
Sbjct: 212 SHTTMINGLGVVGWGVGGIEAEACMLGQPLYFITPEVIGFKLTGQLPDGATATDLALTVT 271

Query: 265 EFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGR 324
           E LR + VV  ++EF+G G   L+L DRAT++NM PE+GAT   F +D + L+YL  TGR
Sbjct: 272 EMLRKKGVVGKFVEFYGPGLSNLSLADRATVANMAPEYGATIGFFPVDDEALNYLRNTGR 331

Query: 325 EAEQVKLVETYAKTAGLW-SDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAA 383
           + E V LV+ Y +  GL+ +DD    V+  T+  DLS+VV +++GP  P  R+  + +  
Sbjct: 332 DEELVTLVKEYYQAQGLFRTDDTPDPVFTDTVELDLSTVVPSLSGPKRPQDRIELTAMKE 391

Query: 384 R--------------GISGE--VENEPGLMPDG--------AVIIAAITSCTNTSNPRNV 419
                          G+S E   ++    +PDG        AV+IAAITSCTNTSNP  +
Sbjct: 392 AWNETLRKPIDQRGFGLSEEECAKSAQVSLPDGSTYQLDQGAVVIAAITSCTNTSNPSVM 451

Query: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479
           + AGL+A+ A  KGLT KP+VK+SL PGSK V  YL++A L+  L  LGF + G+ C TC
Sbjct: 452 VGAGLVAKKAVEKGLTVKPFVKSSLTPGSKVVTDYLDKAGLIEPLAKLGFTVAGYGCATC 511

Query: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539
            G SG L   + + + + DL   +VLSGNRNF+GRIHP  K  +LASPPLVVAYA+AGT+
Sbjct: 512 IGNSGPLSDEVSKAIEENDLTVASVLSGNRNFEGRIHPLVKANYLASPPLVVAYALAGTV 571

Query: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599
             D   + +G +  G+ + L +IWPS  EI  V+ +++  EQFRK Y  +FD +  +   
Sbjct: 572 NIDFATEPIGHNDAGEAIYLKDIWPSSHEISQVMNSAISAEQFRKQYAQVFDANERWNQL 631

Query: 600 VSP---LYDWRPQSTYIRRPPYWEGALAGERTLK---GMRPLAVLGDNITTDHLSPSNAI 653
            +P   LY+W   STYI+ PP++    A    +K   G   LA+L D++TTDH+SP+ +I
Sbjct: 632 PTPKGVLYEWDQDSTYIQEPPFFVDMSADVEEIKPITGAHILALLNDSVTTDHISPAGSI 691

Query: 654 MMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLA 713
              S AG YL   G+  +DFNSY + RG+     R TFAN +++N+M  V G   +G + 
Sbjct: 692 APTSPAGRYLQDKGVAIKDFNSYGSRRGNDRVMTRGTFANIRIRNQM--VPG--SEGGVT 747

Query: 714 RIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFE 773
           +  P   V  +++A   Y     PL++IAG +YG GSSRDWAAKG  L GV+A++AE FE
Sbjct: 748 KHVPSQQVMSIYDAAMEYKKSGTPLVVIAGKEYGTGSSRDWAAKGTNLLGVKAVIAESFE 807

Query: 774 RIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIITRKNGER 830
           RIHR+NLVGMGVLPL+F  G N  + G+DGTE  D+ G    + P   LTV  T+ +G  
Sbjct: 808 RIHRSNLVGMGVLPLQFANGANWQSLGLDGTEKIDIAGLNDEVTPGQTLTVTATKPDGSS 867

Query: 831 VEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFL 862
           V+  VT RLD+  ++  Y  GG+LQ   +  L
Sbjct: 868 VQFDVTVRLDSVVDIEYYRNGGILQTVLRQIL 899


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: 1925
Number of extensions: 92
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: 907
Length adjustment: 43
Effective length of query: 824
Effective length of database: 864
Effective search space:   711936
Effective search space used:   711936
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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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