GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Pontibacillus litoralis JSM 072002

Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate WP_036833565.1 N784_RS06830 bifunctional 2-methylcitrate dehydratase/aconitate hydratase

Query= SwissProt::P45859
         (472 letters)



>NCBI__GCF_000775615.1:WP_036833565.1
          Length = 480

 Score =  690 bits (1781), Expect = 0.0
 Identities = 326/467 (69%), Positives = 388/467 (83%)

Query: 4   TDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTTVP 63
           TD+V+E+I DY +  +I S EA+ TA +VL+DT+GCG+LAL+YPECTK LGPIVPGT VP
Sbjct: 12  TDQVLEQIADYAINGQIKSEEAWQTARYVLMDTIGCGVLALKYPECTKHLGPIVPGTVVP 71

Query: 64  NGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSRVR 123
           NG  VPGTSY LDPV AAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGG+LA ADY+S+ R
Sbjct: 72  NGVHVPGTSYKLDPVHAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGVLAVADYISQKR 131

Query: 124 LSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGGGR 183
           LSEGK P+ +  VLE  +KAHEIQG+LALENSLNR GLDHVLFVKVATTAV   +LGG +
Sbjct: 132 LSEGKAPIRMETVLEYTVKAHEIQGILALENSLNRQGLDHVLFVKVATTAVVTAMLGGNK 191

Query: 184 EEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTALS 243
           +++ NA+S AW+DN++LRTYRH+PNTGSRKSWAAGDATSRGV LA+M++ GEMGY TALS
Sbjct: 192 QDVVNAVSQAWLDNSSLRTYRHAPNTGSRKSWAAGDATSRGVRLAMMTMFGEMGYKTALS 251

Query: 244 APGWGFQDVLFNKKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAAESAVILHPQVKNRI 303
           APGWGFQDVL N +E+ LA+ LD+YVMEN+LFK+ YPAEFHAQTA E+A+ LH +VK+R+
Sbjct: 252 APGWGFQDVLMNGQELTLAQDLDSYVMENILFKIKYPAEFHAQTAVEAAIQLHHEVKDRL 311

Query: 304 DEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGDITAQHYEAETANDP 363
           +EI +V I THESAIRIIDK GPLHNPADRDHCLQYITAIGL++G++TA HYE  TA  P
Sbjct: 312 EEIHKVTITTHESAIRIIDKTGPLHNPADRDHCLQYITAIGLIYGELTADHYEDATARHP 371

Query: 364 RIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEMVECEFPLGHRFRREE 423
           +ID+LR+KME  ENK Y+ DYL  +KRSI+NAVQVHF DGTSTE V+ E+P+GHR RREE
Sbjct: 372 QIDRLREKMETVENKQYSADYLDANKRSIANAVQVHFTDGTSTEQVKIEYPIGHRRRREE 431

Query: 424 AVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVDMF 470
            +P LL KF  NLKT FP +Q   I   C  ++ L    VNEF+DMF
Sbjct: 432 GLPLLLNKFQSNLKTRFPLRQVNQILNLCEDHDVLMRKPVNEFMDMF 478


Lambda     K      H
   0.319    0.135    0.402 

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: 752
Number of extensions: 18
Number of successful extensions: 1
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: 472
Length of database: 480
Length adjustment: 33
Effective length of query: 439
Effective length of database: 447
Effective search space:   196233
Effective search space used:   196233
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_036833565.1 N784_RS06830 (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.3175498.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-260  849.2   0.1   4.5e-260  849.0   0.1    1.0  1  NCBI__GCF_000775615.1:WP_036833565.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036833565.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  849.0   0.1  4.5e-260  4.5e-260       1     468 []      13     480 .]      13     480 .] 1.00

  Alignments for each domain:
  == domain 1  score: 849.0 bits;  conditional E-value: 4.5e-260
                             TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldp 73 
                                           d+vle+iady+++ +i+s+ea++taryvl+dt+gcg+lal+ypectk+lgp+v+gt+vpng++vpgtsy+ldp
  NCBI__GCF_000775615.1:WP_036833565.1  13 DQVLEQIADYAINGQIKSEEAWQTARYVLMDTIGCGVLALKYPECTKHLGPIVPGTVVPNGVHVPGTSYKLDP 85 
                                           899********************************************************************** PP

                             TIGR02330  74 vkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvl 146
                                           v+aafnig+++rwldyndtwlaaewghpsdnlgg+lavady+s+kr++egk+p+++  vle  +kaheiqg+l
  NCBI__GCF_000775615.1:WP_036833565.1  86 VHAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGVLAVADYISQKRLSEGKAPIRMETVLEYTVKAHEIQGIL 158
                                           ************************************************************************* PP

                             TIGR02330 147 alensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsr 219
                                           alens+nr gldhvl+vkva+tavv+++lg+++++++na+s+a++d+++lrtyrhapntgsrkswaagdatsr
  NCBI__GCF_000775615.1:WP_036833565.1 159 ALENSLNRQGLDHVLFVKVATTAVVTAMLGGNKQDVVNAVSQAWLDNSSLRTYRHAPNTGSRKSWAAGDATSR 231
                                           ************************************************************************* PP

                             TIGR02330 220 gvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfpaefhaqtaveaavklh 292
                                           gvrla++++ gemgy +alsap wgf+dvl+++++l+la++++syvmen+lfki +paefhaqtaveaa++lh
  NCBI__GCF_000775615.1:WP_036833565.1 232 GVRLAMMTMFGEMGYKTALSAPGWGFQDVLMNGQELTLAQDLDSYVMENILFKIKYPAEFHAQTAVEAAIQLH 304
                                           ************************************************************************* PP

                             TIGR02330 293 eevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyedavaadpridelr 365
                                           +evk+rl+ei++++itthesairiidk+gpl npadrdhclqy++a++l++g+l+a++yeda a++p+id+lr
  NCBI__GCF_000775615.1:WP_036833565.1 305 HEVKDRLEEIHKVTITTHESAIRIIDKTGPLHNPADRDHCLQYITAIGLIYGELTADHYEDATARHPQIDRLR 377
                                           ************************************************************************* PP

                             TIGR02330 366 eklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfss 438
                                           ek+e ve+k+ys++yl+a+krsianav+v+f+dg++te+v++eyp+ghrrrr+eg+p+l +kf+ nl t+f+ 
  NCBI__GCF_000775615.1:WP_036833565.1 378 EKMETVENKQYSADYLDANKRSIANAVQVHFTDGTSTEQVKIEYPIGHRRRREEGLPLLLNKFQSNLKTRFPL 450
                                           ************************************************************************* PP

                             TIGR02330 439 kkqerilelcldqakleatpvnefldlfvi 468
                                           ++ ++il+lc d++ l + pvnef+d+f i
  NCBI__GCF_000775615.1:WP_036833565.1 451 RQVNQILNLCEDHDVLMRKPVNEFMDMFTI 480
                                           ***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (480 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: 00:00:00.00
# Mc/sec: 23.94
//
[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:

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:

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:

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:

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