Alignments for a candidate for prpD in Granulicella mallensis MP5ACTX8

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Granulicella mallensis MP5ACTX8

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate WP_044175992.1 ACIX8_RS01660 bifunctional 2-methylcitrate dehydratase/aconitate hydratase

Query= BRENDA::P77243
         (483 letters)



>NCBI__GCF_000178955.2:WP_044175992.1
          Length = 482

 Score =  758 bits (1957), Expect = 0.0
 Identities = 368/487 (75%), Positives = 423/487 (86%), Gaps = 9/487 (1%)

Query: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MS+ I+N+RPEFD+ ++DIVDYV+NY+I S +AY+TA YCLLDTLGCGL+AL++PAC KL
Sbjct: 1   MSSHISNVRPEFDQPLIDIVDYVLNYKIESPLAYETARYCLLDTLGCGLQALDFPACTKL 60

Query: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           LGP+VPG  + NG RVPGT ++LDPVQAAFNIG +IRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  LGPLVPGLTMHNGARVPGTGYELDPVQAAFNIGTIIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180
           LA ADWLSRN        LTM+ VLTAMIKAHEIQGC+ALENSFN+VGLDHV+LVKVAST
Sbjct: 121 LAVADWLSRN-----DKRLTMRDVLTAMIKAHEIQGCLALENSFNKVGLDHVVLVKVAST 175

Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVVA+MLGL RE+ILNAVSLAWVDGQSLRTYRHAPN G+RKSWAAGDATSRAVRLAL+A+
Sbjct: 176 AVVAQMLGLPREQILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRAVRLALIAQ 235

Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPS L+A  WGFYDVSFKG+ F+FQRPYGSYVMENVLFKISFPAEFHSQTAVEAA
Sbjct: 236 TGEMGYPSVLSAKTWGFYDVSFKGQPFKFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 295

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360
           MTL+ Q+ A GKTAADI++VTIRTHEACIRIIDK+GPLNNPADRDHCIQYMVA+PL+FGR
Sbjct: 296 MTLHAQLAAMGKTAADIKRVTIRTHEACIRIIDKQGPLNNPADRDHCIQYMVAVPLIFGR 355

Query: 361 LTAADYEDNVAQD----KRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTR 416
           LTA DYED VA+D     RIDA+R +I C EDP +TADYHDPEKR+IANA+T+E +DGT 
Sbjct: 356 LTAEDYEDAVARDTTWGPRIDAVRARIVCVEDPQYTADYHDPEKRSIANALTVELSDGTV 415

Query: 417 FEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNE 476
             EV VEYPIGH  RR DGIP L+DKF+ NL R+     QQ+IL  S ++A+LE MPV+E
Sbjct: 416 LPEVAVEYPIGHRLRRGDGIPLLLDKFRQNLERRLSPEAQQKILAASSEQAKLEAMPVDE 475

Query: 477 YLDLYVI 483
           Y+ LY +
Sbjct: 476 YVGLYTV 482


Lambda     K      H
   0.321    0.136    0.406 

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: 784
Number of extensions: 15
Number of successful extensions: 3
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: 483
Length of database: 482
Length adjustment: 34
Effective length of query: 449
Effective length of database: 448
Effective search space:   201152
Effective search space used:   201152
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_044175992.1 ACIX8_RS01660 (bifunctional 2-methylcitrate dehydratase/aconitate hydratase)
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02330.hmm
# target sequence database:        /tmp/gapView.214336.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02330  [M=468]
Accession:   TIGR02330
Description: prpD: 2-methylcitrate dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-251  820.9   0.0   1.7e-251  820.7   0.0    1.0  1  NCBI__GCF_000178955.2:WP_044175992.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000178955.2:WP_044175992.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.7   0.0  1.7e-251  1.7e-251       1     467 [.      13     481 ..      13     482 .] 0.98

  Alignments for each domain:
  == domain 1  score: 820.7 bits;  conditional E-value: 1.7e-251
                             TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldp 73 
                                           d+ l di+dyvl+y+i+s++ay+tary+lldtlgcgl+al++p+ctkllgp+v+g  + ngarvpgt y+ldp
  NCBI__GCF_000178955.2:WP_044175992.1  13 DQPLIDIVDYVLNYKIESPLAYETARYCLLDTLGCGLQALDFPACTKLLGPLVPGLTMHNGARVPGTGYELDP 85 
                                           66789******************************************************************** PP

                             TIGR02330  74 vkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvl 146
                                           v+aafnig+++rwld+ndtwlaaewghpsdnlggilavad+lsr+     ++ l++++vl+amikaheiqg+l
  NCBI__GCF_000178955.2:WP_044175992.1  86 VQAAFNIGTIIRWLDFNDTWLAAEWGHPSDNLGGILAVADWLSRN-----DKRLTMRDVLTAMIKAHEIQGCL 153
                                           *******************************************98.....578******************** PP

                             TIGR02330 147 alensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsr 219
                                           alensfn+vgldhv+lvkvastavva++lg+ re+ilna+s+a+vdgq+lrtyrhapn+gsrkswaagdatsr
  NCBI__GCF_000178955.2:WP_044175992.1 154 ALENSFNKVGLDHVVLVKVASTAVVAQMLGLPREQILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAAGDATSR 226
                                           ************************************************************************* PP

                             TIGR02330 220 gvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfpaefhaqtaveaavklh 292
                                           +vrlalia++gemgyps+lsa +wgf+dv+fk++ +k++r+ygsyvmenvlfkisfpaefh+qtaveaa++lh
  NCBI__GCF_000178955.2:WP_044175992.1 227 AVRLALIAQTGEMGYPSVLSAKTWGFYDVSFKGQPFKFQRPYGSYVMENVLFKISFPAEFHSQTAVEAAMTLH 299
                                           ************************************************************************* PP

                             TIGR02330 293 eevker...ldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyedavaad.... 358
                                            ++ +    +++i+r++i+the++iriidk+gpl+npadrdhc+qy+vavpl+fg+l+aedyedava+d    
  NCBI__GCF_000178955.2:WP_044175992.1 300 AQLAAMgktAADIKRVTIRTHEACIRIIDKQGPLNNPADRDHCIQYMVAVPLIFGRLTAEDYEDAVARDttwg 372
                                           99876555599********************************************************986666 PP

                             TIGR02330 359 pridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkan 431
                                           prid++r ++++ved++y+++y++++krsiana++v+ +dg++  ev+veyp+ghr rr +gip+l dkf++n
  NCBI__GCF_000178955.2:WP_044175992.1 373 PRIDAVRARIVCVEDPQYTADYHDPEKRSIANALTVELSDGTVLPEVAVEYPIGHRLRRGDGIPLLLDKFRQN 445
                                           8************************************************************************ PP

                             TIGR02330 432 latkfsskkqerilelcldqakleatpvnefldlfv 467
                                           l +++s++ q++il  +++qaklea+pv+e++ l+ 
  NCBI__GCF_000178955.2:WP_044175992.1 446 LERRLSPEAQQKILAASSEQAKLEAMPVDEYVGLYT 481
                                           **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (482 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.33
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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