Alignments for a candidate for prpD in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Halomonas desiderata SP1

Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate WP_086511662.1 BZY95_RS20075 2-methylcitrate dehydratase

Query= SwissProt::P45859
         (472 letters)



>NCBI__GCF_002151265.1:WP_086511662.1
          Length = 494

 Score =  613 bits (1582), Expect = e-180
 Identities = 301/482 (62%), Positives = 373/482 (77%), Gaps = 13/482 (2%)

Query: 2   PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61
           P  D  +++I DYVL+  I S EA  TA H L+DTLGCG+LALR+PEC K LGP+V GT 
Sbjct: 11  PDYDPELQKIADYVLDYRIASEEALETARHCLVDTLGCGLLALRFPECIKHLGPLVEGTV 70

Query: 62  VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121
           VPNG++VPGT++ LDPV+AA++IGC++RWLDYNDTWLAAEWGHPSDNLG ILA AD++S+
Sbjct: 71  VPNGARVPGTAFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGAILAVADHLSQ 130

Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181
            R+++G+ PLT+RDVLE MIKAHEIQGVLALENS NRVGLDHV+ VKVA+TAVAA L+G 
Sbjct: 131 KRVAQGEAPLTMRDVLEAMIKAHEIQGVLALENSFNRVGLDHVVLVKVASTAVAAHLMGA 190

Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241
            RE++ +ALS+AW+D  +LRTYRH+PN GSRKSWAAGDATSRGV LA ++L+GEMG P  
Sbjct: 191 SREQLLSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRGVRLADIALRGEMGVPGV 250

Query: 242 LSAPGWGFQDVLFNK------------KEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289
           LSAP WGF DVLF+K            ++ +  R    YVMEN+LFK+++PAEFHAQTA 
Sbjct: 251 LSAPQWGFYDVLFSKTNKDQAIKPEGERKFRFQREFGTYVMENILFKIAFPAEFHAQTAC 310

Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349
           E+AV LHPQVK+R+ EI RVVI THESAIRII K+G L NPADRDHCLQY+ A+ L+FGD
Sbjct: 311 EAAVRLHPQVKDRLAEIQRVVITTHESAIRIISKEGELANPADRDHCLQYMVAVPLIFGD 370

Query: 350 ITAQHYEAE-TANDPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408
           +TA+HYE +     P ID LRDKMEV E   YT++YL  DKRSI+NA+QV F DGT+TE 
Sbjct: 371 LTAEHYEDDFHRQHPLIDVLRDKMEVVEEPRYTQEYLAADKRSIANAIQVFFSDGTATEC 430

Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468
           +E E+P+GHR RR+E +P L EKF  +L T FP  + + I   C     L+ M V+ FVD
Sbjct: 431 IEVEYPIGHRRRRDEGIPILEEKFRRHLATRFPAGRCERIIALCQDQAQLEAMPVHRFVD 490

Query: 469 MF 470
           +F
Sbjct: 491 LF 492


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: 701
Number of extensions: 26
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: 472
Length of database: 494
Length adjustment: 34
Effective length of query: 438
Effective length of database: 460
Effective search space:   201480
Effective search space used:   201480
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: 52 (24.6 bits)

Align candidate WP_086511662.1 BZY95_RS20075 (2-methylcitrate dehydratase)
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.7330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-268  877.5   0.0   1.2e-268  877.3   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511662.1  BZY95_RS20075 2-methylcitrate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511662.1  BZY95_RS20075 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.3   0.0  1.2e-268  1.2e-268       1     468 []      14     494 .]      14     494 .] 0.99

  Alignments for each domain:
  == domain 1  score: 877.3 bits;  conditional E-value: 1.2e-268
                                 TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsy 69 
                                               d +l++iadyvl+y+i s+ea++tar++l+dtlgcgllal++pec k+lgp+vegt+vpngarvpgt++
  lcl|NCBI__GCF_002151265.1:WP_086511662.1  14 DPELQKIADYVLDYRIASEEALETARHCLVDTLGCGLLALRFPECIKHLGPLVEGTVVPNGARVPGTAF 82 
                                               5689***************************************************************** PP

                                 TIGR02330  70 qldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamik 138
                                               +ldpvkaa++ig++vrwldyndtwlaaewghpsdnlg+ilavad+ls+kr+a+g++pl++++vleamik
  lcl|NCBI__GCF_002151265.1:WP_086511662.1  83 RLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGAILAVADHLSQKRVAQGEAPLTMRDVLEAMIK 151
                                               ********************************************************************* PP

                                 TIGR02330 139 aheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgs 207
                                               aheiqgvlalensfnrvgldhv+lvkvastav+a+l+ga+re++l+alsha+vdgq+lrtyrhapn+gs
  lcl|NCBI__GCF_002151265.1:WP_086511662.1 152 AHEIQGVLALENSFNRVGLDHVVLVKVASTAVAAHLMGASREQLLSALSHAWVDGQSLRTYRHAPNAGS 220
                                               ********************************************************************* PP

                                 TIGR02330 208 rkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkke............klklareygsy 264
                                               rkswaagdatsrgvrla+ial+gemg+p++lsap+wgf+dvlf+k+            k++++re+g+y
  lcl|NCBI__GCF_002151265.1:WP_086511662.1 221 RKSWAAGDATSRGVRLADIALRGEMGVPGVLSAPQWGFYDVLFSKTnkdqaikpegerKFRFQREFGTY 289
                                               *********************************************99********************** PP

                                 TIGR02330 265 vmenvlfkisfpaefhaqtaveaavklheevkerldeierivitthesairiidkkgplanpadrdhcl 333
                                               vmen+lfki+fpaefhaqta+eaav+lh++vk+rl+ei+r+vitthesairii+k+g lanpadrdhcl
  lcl|NCBI__GCF_002151265.1:WP_086511662.1 290 VMENILFKIAFPAEFHAQTACEAAVRLHPQVKDRLAEIQRVVITTHESAIRIISKEGELANPADRDHCL 358
                                               ********************************************************************* PP

                                 TIGR02330 334 qylvavpllfgdlvaedyeda.vaadpridelreklevvedkrysreyleadkrsianavevffkdgsk 401
                                               qy+vavpl+fgdl+ae+yed  + ++p+id lr+k+evve++ry++eyl adkrsiana++vff+dg+ 
  lcl|NCBI__GCF_002151265.1:WP_086511662.1 359 QYMVAVPLIFGDLTAEHYEDDfHRQHPLIDVLRDKMEVVEEPRYTQEYLAADKRSIANAIQVFFSDGTA 427
                                               *******************99899********************************************* PP

                                 TIGR02330 402 teeveveyplghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                               te +eveyp+ghrrrrdegip+l +kf++ lat+f++ ++eri  lc dqa+lea+pv +f+dlfvi
  lcl|NCBI__GCF_002151265.1:WP_086511662.1 428 TECIEVEYPIGHRRRRDEGIPILEEKFRRHLATRFPAGRCERIIALCQDQAQLEAMPVHRFVDLFVI 494
                                               *****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (494 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.65
//
[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