Alignments for a candidate for prpD in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Marinobacter adhaerens HP15

Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate GFF1971 HP15_1928 2-methylcitrate dehydratase PrpD

Query= SwissProt::P45859
         (472 letters)



>FitnessBrowser__Marino:GFF1971
          Length = 494

 Score =  605 bits (1559), Expect = e-177
 Identities = 294/481 (61%), Positives = 378/481 (78%), Gaps = 13/481 (2%)

Query: 2   PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61
           P  D V+++I DYVL  EITS EA+ TA + L+DTLGC +LALR+PECTK LGPIV GT 
Sbjct: 11  PDYDEVLQKIADYVLTYEITSEEAWNTARYCLMDTLGCALLALRFPECTKHLGPIVEGTM 70

Query: 62  VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121
           VP+G++VPGT Y LDPV+AA++IGC +RWLDYNDTWLAAEWGHPSDNLG ILA AD++S+
Sbjct: 71  VPHGARVPGTPYRLDPVKAAWDIGCNVRWLDYNDTWLAAEWGHPSDNLGAILAVADHLSQ 130

Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181
            R++EGKEPLT+R VLE MI AHEIQGVLALENS NRVGLDHV+ VKVA+TAVA++L+G 
Sbjct: 131 KRVAEGKEPLTMRTVLEAMIMAHEIQGVLALENSFNRVGLDHVVLVKVASTAVASRLMGA 190

Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241
            RE++ +ALS+AW+D  +LRTYRH+PN GSRKSWAAGDATSR V LA ++++GEMG P  
Sbjct: 191 DREQLLSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRAVRLADIAMRGEMGVPGV 250

Query: 242 LSAPGWGFQDVLF------------NKKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289
           L+AP WGF DVLF            +K++  L +   +YVMEN+LFK+S+PAEFHAQTAA
Sbjct: 251 LTAPQWGFYDVLFSKTNKDQKLKPEDKRQFSLPQEFGSYVMENILFKISFPAEFHAQTAA 310

Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349
           E+AVIL+P+VK+R++EI+++VI THESAIRII K G L N ADRDHCLQY+ A+ L FG 
Sbjct: 311 EAAVILYPEVKDRLNEINKIVITTHESAIRIISKVGKLANAADRDHCLQYMAAVPLAFGS 370

Query: 350 ITAQHYEAETAN-DPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408
           +TA+HYE      +P ID+LRDKMEV E++ YT +YL+P+KRSI+NA+QV F DG++T+ 
Sbjct: 371 LTAEHYEDSFHRANPIIDELRDKMEVVEDERYTREYLEPEKRSIANAIQVFFNDGSNTDK 430

Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468
           +  E+P+GHR RR+E +P L EKF  NLKT  P K+   + + C   E L+   V+EF++
Sbjct: 431 IAVEYPIGHRRRRKEGMPLLEEKFLSNLKTRLPSKRCDTVLKMCQDPEKLENTPVHEFMN 490

Query: 469 M 469
           +
Sbjct: 491 L 491


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: 676
Number of extensions: 23
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 GFF1971 HP15_1928 (2-methylcitrate dehydratase PrpD)
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.9573.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.4e-264  861.7   0.0   7.2e-264  861.5   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1971  HP15_1928 2-methylcitrate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1971  HP15_1928 2-methylcitrate dehydratase PrpD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  861.5   0.0  7.2e-264  7.2e-264       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 861.5 bits;  conditional E-value: 7.2e-264
                           TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldpvk 75 
                                         d+vl++iadyvl yei+s+ea++tary+l+dtlgc llal++pectk+lgp+vegt+vp+garvpgt y+ldpvk
  lcl|FitnessBrowser__Marino:GFF1971  14 DEVLQKIADYVLTYEITSEEAWNTARYCLMDTLGCALLALRFPECTKHLGPIVEGTMVPHGARVPGTPYRLDPVK 88 
                                         89************************************************************************* PP

                           TIGR02330  76 aafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvlalen 150
                                         aa++ig+ vrwldyndtwlaaewghpsdnlg+ilavad+ls+kr+aegkepl+++ vleami+aheiqgvlalen
  lcl|FitnessBrowser__Marino:GFF1971  89 AAWDIGCNVRWLDYNDTWLAAEWGHPSDNLGAILAVADHLSQKRVAEGKEPLTMRTVLEAMIMAHEIQGVLALEN 163
                                         *************************************************************************** PP

                           TIGR02330 151 sfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsrgvrlal 225
                                         sfnrvgldhv+lvkvastav+++l+ga+re++l+alsha+vdgq+lrtyrhapn+gsrkswaagdatsr+vrla+
  lcl|FitnessBrowser__Marino:GFF1971 164 SFNRVGLDHVVLVKVASTAVASRLMGADREQLLSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRAVRLAD 238
                                         *************************************************************************** PP

                           TIGR02330 226 ialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefhaqtaveaa 288
                                         ia++gemg+p++l+ap+wgf+dvlf+k+            +++l++e+gsyvmen+lfkisfpaefhaqta+eaa
  lcl|FitnessBrowser__Marino:GFF1971 239 IAMRGEMGVPGVLTAPQWGFYDVLFSKTnkdqklkpedkrQFSLPQEFGSYVMENILFKISFPAEFHAQTAAEAA 313
                                         **************************999********************************************** PP

                           TIGR02330 289 vklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadprid 362
                                         v l++evk+rl+ei++ivitthesairii+k+g lan adrdhclqy++avpl fg l+ae+yed+ + a+p id
  lcl|FitnessBrowser__Marino:GFF1971 314 VILYPEVKDRLNEINKIVITTHESAIRIISKVGKLANAADRDHCLQYMAAVPLAFGSLTAEHYEDSfHRANPIID 388
                                         ******************************************************************8999***** PP

                           TIGR02330 363 elreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfs 437
                                         elr+k+evved+ry+reyle++krsiana++vff+dgs+t++++veyp+ghrrrr+eg+p+l +kf  nl t+++
  lcl|FitnessBrowser__Marino:GFF1971 389 ELRDKMEVVEDERYTREYLEPEKRSIANAIQVFFNDGSNTDKIAVEYPIGHRRRRKEGMPLLEEKFLSNLKTRLP 463
                                         *************************************************************************** PP

                           TIGR02330 438 skkqerilelcldqakleatpvnefldlfvi 468
                                         sk+++ +l++c d +kle+tpv ef++l++i
  lcl|FitnessBrowser__Marino:GFF1971 464 SKRCDTVLKMCQDPEKLENTPVHEFMNLLLI 494
                                         ****************************986 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: 00:00:00.02
# Mc/sec: 8.50
//
[ok]

This GapMind analysis is from Sep 17 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