GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Marinobacter algicola DG893

Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate WP_007152510.1 MDG893_RS04350 2-methylcitrate dehydratase

Query= SwissProt::P45859
         (472 letters)



>NCBI__GCF_000170835.1:WP_007152510.1
          Length = 494

 Score =  617 bits (1590), Expect = 0.0
 Identities = 299/482 (62%), Positives = 379/482 (78%), Gaps = 13/482 (2%)

Query: 2   PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61
           P  D V++ I DY L   I S EA+ TA + L+DT+GCG+LALR+PECTK LGP+V GT 
Sbjct: 11  PDYDDVLQAIADYTLGYRIKSKEAWNTARNCLMDTIGCGLLALRFPECTKHLGPLVDGTV 70

Query: 62  VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121
           VP+G++VPGT Y LDPV+AA++IGC++RWLDYNDTWLAAEWGHPSDNLGGILA AD++S+
Sbjct: 71  VPHGARVPGTPYKLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQ 130

Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181
            R++EGK PLTVRDVLE MI AHEIQGVLALENS NRVGLDHV+ VKVA+TAV AKL+G 
Sbjct: 131 KRVAEGKAPLTVRDVLEAMIMAHEIQGVLALENSFNRVGLDHVVLVKVASTAVTAKLMGA 190

Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241
            R+++ +ALS+AW+D  ALRTYRH+PN GSRKSWAAGDATSR V LA ++++GEMG P+ 
Sbjct: 191 SRDQMLSALSHAWVDGQALRTYRHAPNAGSRKSWAAGDATSRAVRLADIAMRGEMGIPSV 250

Query: 242 LSAPGWGFQDVLF------------NKKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289
           L+AP WGF D+LF            +K++  L +   AYVMEN+LFK+S+PAEFHAQTAA
Sbjct: 251 LTAPQWGFYDILFSKTNKDQTLKPEDKRQFTLPQAFGAYVMENILFKISFPAEFHAQTAA 310

Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349
           E+AVILHP+VK+R+DEI+R+VI THESAIRII K+G L N ADRDHCLQY+ A+ L+FG 
Sbjct: 311 EAAVILHPEVKDRLDEIERIVITTHESAIRIISKQGKLANAADRDHCLQYMAAVPLIFGG 370

Query: 350 ITAQHYEAETAN-DPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408
           +TA+HYE      +P ID++RDKMEV E++ YT +YL+ DKRSI+NA+QV F DGTST+ 
Sbjct: 371 LTAEHYEDSFHEANPLIDQIRDKMEVVEDERYTREYLEADKRSIANAIQVFFTDGTSTDN 430

Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468
           V  E+P+GHR RR+E +P L +KF  NL T FP ++ + I++ C     L+   V+EFV 
Sbjct: 431 VAVEYPIGHRRRRKEGIPLLEDKFRHNLATRFPGQRCEKIFQLCKDQTELEATPVHEFVG 490

Query: 469 MF 470
           MF
Sbjct: 491 MF 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: 696
Number of extensions: 21
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_007152510.1 MDG893_RS04350 (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.2887430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-267  872.1   0.0   5.2e-267  871.9   0.0    1.0  1  NCBI__GCF_000170835.1:WP_007152510.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170835.1:WP_007152510.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.9   0.0  5.2e-267  5.2e-267       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 871.9 bits;  conditional E-value: 5.2e-267
                             TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldp 73 
                                           d+vl+ iady l y+i+skea++tar++l+dt+gcgllal++pectk+lgp+v+gt+vp+garvpgt y+ldp
  NCBI__GCF_000170835.1:WP_007152510.1  14 DDVLQAIADYTLGYRIKSKEAWNTARNCLMDTIGCGLLALRFPECTKHLGPLVDGTVVPHGARVPGTPYKLDP 86 
                                           789********************************************************************** PP

                             TIGR02330  74 vkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvl 146
                                           vkaa++ig++vrwldyndtwlaaewghpsdnlggilavad+ls+kr+aegk+pl+v++vleami+aheiqgvl
  NCBI__GCF_000170835.1:WP_007152510.1  87 VKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQKRVAEGKAPLTVRDVLEAMIMAHEIQGVL 159
                                           ************************************************************************* PP

                             TIGR02330 147 alensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsr 219
                                           alensfnrvgldhv+lvkvastav+akl+ga+r+++l+alsha+vdgqalrtyrhapn+gsrkswaagdatsr
  NCBI__GCF_000170835.1:WP_007152510.1 160 ALENSFNRVGLDHVVLVKVASTAVTAKLMGASRDQMLSALSHAWVDGQALRTYRHAPNAGSRKSWAAGDATSR 232
                                           ************************************************************************* PP

                             TIGR02330 220 gvrlalialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefh 280
                                           +vrla+ia++gemg+ps+l+ap+wgf+d+lf+k+            +++l++ +g+yvmen+lfkisfpaefh
  NCBI__GCF_000170835.1:WP_007152510.1 233 AVRLADIAMRGEMGIPSVLTAPQWGFYDILFSKTnkdqtlkpedkrQFTLPQAFGAYVMENILFKISFPAEFH 305
                                           ********************************999************************************** PP

                             TIGR02330 281 aqtaveaavklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyed 353
                                           aqta+eaav lh+evk+rldeierivitthesairii+k+g lan adrdhclqy++avpl+fg l+ae+yed
  NCBI__GCF_000170835.1:WP_007152510.1 306 AQTAAEAAVILHPEVKDRLDEIERIVITTHESAIRIISKQGKLANAADRDHCLQYMAAVPLIFGGLTAEHYED 378
                                           ************************************************************************* PP

                             TIGR02330 354 a.vaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklv 425
                                           + + a+p+id++r+k+evved+ry+reyleadkrsiana++vff+dg++t++v+veyp+ghrrrr+egip+l 
  NCBI__GCF_000170835.1:WP_007152510.1 379 SfHEANPLIDQIRDKMEVVEDERYTREYLEADKRSIANAIQVFFTDGTSTDNVAVEYPIGHRRRRKEGIPLLE 451
                                           *8899******************************************************************** PP

                             TIGR02330 426 dkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                           dkf+ nlat+f+ +++e+i++lc dq +leatpv ef+ +fvi
  NCBI__GCF_000170835.1:WP_007152510.1 452 DKFRHNLATRFPGQRCEKIFQLCKDQTELEATPVHEFVGMFVI 494
                                           ****************************************997 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.41
//
[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