Alignments for a candidate for acnD in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Nocardioides dokdonensis FR1436

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_068112647.1 I601_RS17670 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001653335.1:WP_068112647.1
          Length = 936

 Score =  679 bits (1752), Expect = 0.0
 Identities = 381/906 (42%), Positives = 527/906 (58%), Gaps = 86/906 (9%)

Query: 36  AKLPYTSRVLAENLVRRCEPEMLTASLKQII-------ESKQELDFPWFPARVVCHDILG 88
           A LP++ +VL ENL+R  +   +TA   + I       +  QE+ F   PARV+  D  G
Sbjct: 36  ASLPFSLKVLLENLLRTEDGSDITADDVKAIAGWDADADPSQEIQFT--PARVIMQDFTG 93

Query: 89  QTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRR 148
              +VDLA +R+A+A  GGDP ++NP+ P ++++DHS+  +  G   +AF +N  IE  R
Sbjct: 94  VPCVVDLATMREAMADLGGDPTKINPLAPAEMVIDHSVIADVFG-TPEAFGRNVEIEYER 152

Query: 149 NEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR--NGV--AFPDTLVGTD 204
           N +R+ F+ W Q AF +  V+P G GI+HQ+N+E ++  +  R  +GV  A+PDT VGTD
Sbjct: 153 NRERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIEHLARTVFTREVDGVLQAYPDTCVGTD 212

Query: 205 SHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALT 264
           SHT  V+ +GV+  GVGG+EAE+ MLG+   M +P ++G +L G    G TATD+VL +T
Sbjct: 213 SHTTMVNGIGVVGWGVGGIEAEAAMLGQPVSMLIPRVVGFKLNGDLPEGATATDLVLTIT 272

Query: 265 EFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGR 324
           E LR   VV  ++EF+G G   L L +RATI NM+PEFG+T A+F ID++T  YL LTGR
Sbjct: 273 EMLREHGVVGKFVEFYGPGVSVLPLANRATIGNMSPEFGSTIAVFPIDEETTKYLELTGR 332

Query: 325 EAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAG---------------- 368
             EQ+ LVE YAK  GLW D   +  +   L  DL++VV ++AG                
Sbjct: 333 TPEQIALVEAYAKEQGLWHDPDAEPRFSEKLELDLATVVPSLAGPKRPQDRVSLSEAKES 392

Query: 369 ---------------------------------PSNPHARVPTSE--LAARGISGEVENE 393
                                            P N H   P +    A  G  G   N 
Sbjct: 393 FRSALADYAEDTDAQETKGYDENVEESFPASDTPHNGHGEAPPNGHVAAGSGAGGRPRNP 452

Query: 394 PGL---------MPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSL 444
             +         +  GAV IAAITSCTNTSNP  +I A LLA+ A  KGL RKPWVKT+L
Sbjct: 453 AQVTLADGTSFELDHGAVTIAAITSCTNTSNPSVMIGAALLAKKAVEKGLERKPWVKTTL 512

Query: 445 APGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAV 504
           APGSK V  Y E++ L P L+ LGF +VG+ CTTC G SG L P + Q V D DL   +V
Sbjct: 513 APGSKVVSDYYEKSGLTPYLDKLGFNLVGYGCTTCIGNSGPLIPEVSQAVNDNDLAVVSV 572

Query: 505 LSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWP 564
           LSGNRNF+GRI+P  K  +LASPPLVVAYA+AG++  D+  D LG D +G  V + +IWP
Sbjct: 573 LSGNRNFEGRINPDVKMNYLASPPLVVAYALAGSMDVDLFNDPLGQDTEGNDVYMKDIWP 632

Query: 565 SDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEG 621
           + AEI+ V+A+++  + F   Y  +F     +    +P    ++W  +STY+R+PPY++G
Sbjct: 633 TSAEIEEVVASAITSDMFDDGYADVFAGDEQWRSLPTPEGKTFEWDAESTYVRKPPYFDG 692

Query: 622 ALAGER---TLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYAT 678
                     + G R L  LGD++TTDH+SP+ AI  DS AG YL + G+ + DFNSY +
Sbjct: 693 MPQEPEPVTDIDGARVLLKLGDSVTTDHISPAGAIKKDSPAGHYLAEHGVEQRDFNSYGS 752

Query: 679 HRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARI--EPEGIVTRMWEAIETYMDRKQ 736
            RG+H    R TFAN +L+N+MA       +G   R     E  VT ++EA E Y+    
Sbjct: 753 RRGNHEVMIRGTFANIRLRNQMA----PGTEGGFTRYLDGGEDSVTSVFEASEKYIAAGV 808

Query: 737 PLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENR 796
           PL+++AG +YG GSSRDWAAKG  L GV+A++AE +ERIHR+NL+GMGVLPL++  GE+ 
Sbjct: 809 PLVVLAGKEYGSGSSRDWAAKGTALLGVKAVIAESYERIHRSNLIGMGVLPLQYPEGESA 868

Query: 797 ATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQR 856
            + G+ G E F V G        T    +   + VE     R+DT  E + Y  GG++Q 
Sbjct: 869 ESLGLTGEETFSVSGVTELNDGTTPRTVKVTADGVEFDAVVRIDTPGEANYYRNGGIMQY 928

Query: 857 FAQDFL 862
             ++ L
Sbjct: 929 VLRNLL 934


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: 2121
Number of extensions: 112
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: 936
Length adjustment: 43
Effective length of query: 824
Effective length of database: 893
Effective search space:   735832
Effective search space used:   735832
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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