Alignments for a candidate for prpD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Pseudomonas simiae WCS417

Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate GFF4111 PS417_21060 2-methylcitrate dehydratase

Query= SwissProt::Q937N6
         (484 letters)



>FitnessBrowser__WCS417:GFF4111
          Length = 494

 Score =  594 bits (1531), Expect = e-174
 Identities = 305/497 (61%), Positives = 366/497 (73%), Gaps = 16/497 (3%)

Query: 1   MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60
           MS +     RPD DQ+L DI DYV  Y I S  A DTARNCL+DTLGCGL AL +P CTK
Sbjct: 1   MSANVDQNNRPDYDQLLQDIADYVLNYRIDSRDALDTARNCLMDTLGCGLLALRFPECTK 60

Query: 61  LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120
            LGP+V GT+VP GARVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGG
Sbjct: 61  HLGPIVEGTVVPFGARVPGTSFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGG 120

Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180
           ILA AD +S+  +A G  PLT++AVL AMI AHEIQG IALENSFN+VGLDHV+LVKVAS
Sbjct: 121 ILAVADHLSQKRVANGDVPLTVRAVLEAMIMAHEIQGVIALENSFNRVGLDHVLLVKVAS 180

Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240
           TAV A+++G  R+++L A+S A+VDGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA IA
Sbjct: 181 TAVTAKLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIA 240

Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK------------GQPFRFQRPYGTYVMENILLKISY 288
             GEMG P VL+A  WGFYDVLF              + F   +PYGTYVMEN+L KIS+
Sbjct: 241 MRGEMGIPGVLSAPQWGFYDVLFSHTNKDLALKPEDRRAFSLSQPYGTYVMENVLFKISF 300

Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348
           PAEFHAQTA EAA+ LH           +I  I I THE+ +RII K+G L+N ADRDHC
Sbjct: 301 PAEFHAQTACEAAVTLH---PWVKDRLHEIDRIVITTHESAIRIISKVGQLANAADRDHC 357

Query: 349 IQYMVAVPLLFGRLTAADYEDRI-AADPRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407
           +QYM AVPL FG L A  YED   AA P ID LR ++  VEDP  +R+Y +  KRSIANA
Sbjct: 358 LQYMTAVPLAFGNLVAEQYEDEFHAAHPIIDQLRDKMVIVEDPRYSREYLEADKRSIANA 417

Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467
           + V   DG+  ++V VEYP+GH+RRR EGIPLL +KF+ NLA RF  ++   I A   DQ
Sbjct: 418 VQVFFKDGSCTEQVAVEYPIGHRRRRVEGIPLLEDKFKANLATRFTGQRSAEIFALCKDQ 477

Query: 468 ARLEAMPVNEYLDMYAI 484
           ARLEA PVN ++D++ I
Sbjct: 478 ARLEATPVNRFVDLFVI 494


Lambda     K      H
   0.322    0.136    0.410 

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: 666
Number of extensions: 25
Number of successful extensions: 4
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: 484
Length of database: 494
Length adjustment: 34
Effective length of query: 450
Effective length of database: 460
Effective search space:   207000
Effective search space used:   207000
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 GFF4111 PS417_21060 (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.17278.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.3e-271  885.7   0.0   3.8e-271  885.5   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4111  PS417_21060 2-methylcitrate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4111  PS417_21060 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  885.5   0.0  3.8e-271  3.8e-271       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 885.5 bits;  conditional E-value: 3.8e-271
                           TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldpvk 75 
                                         d++l+diadyvl+y+ids+ a+dtar++l+dtlgcgllal++pectk+lgp+vegt+vp garvpgts++ldpvk
  lcl|FitnessBrowser__WCS417:GFF4111  14 DQLLQDIADYVLNYRIDSRDALDTARNCLMDTLGCGLLALRFPECTKHLGPIVEGTVVPFGARVPGTSFRLDPVK 88 
                                         799************************************************************************ PP

                           TIGR02330  76 aafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvlalen 150
                                         aa++ig++vrwldyndtwlaaewghpsdnlggilavad+ls+kr+a+g+ pl+v+ vleami+aheiqgv+alen
  lcl|FitnessBrowser__WCS417:GFF4111  89 AAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQKRVANGDVPLTVRAVLEAMIMAHEIQGVIALEN 163
                                         *************************************************************************** PP

                           TIGR02330 151 sfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsrgvrlal 225
                                         sfnrvgldhvllvkvastav+akl+ga+re++l+alshafvdgqalrtyrhapn+gsrkswaagda+srgvrla+
  lcl|FitnessBrowser__WCS417:GFF4111 164 SFNRVGLDHVLLVKVASTAVTAKLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLAD 238
                                         *************************************************************************** PP

                           TIGR02330 226 ialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefhaqtaveaa 288
                                         ia++gemg+p++lsap+wgf+dvlf+++             ++l+++yg+yvmenvlfkisfpaefhaqta+eaa
  lcl|FitnessBrowser__WCS417:GFF4111 239 IAMRGEMGIPGVLSAPQWGFYDVLFSHTnkdlalkpedrrAFSLSQPYGTYVMENVLFKISFPAEFHAQTACEAA 313
                                         ***************************99**********99********************************** PP

                           TIGR02330 289 vklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadprid 362
                                         v+lh+ vk+rl+ei+rivitthesairii+k+g lan adrdhclqy++avpl fg+lvae+yed+ +aa+p id
  lcl|FitnessBrowser__WCS417:GFF4111 314 VTLHPWVKDRLHEIDRIVITTHESAIRIISKVGQLANAADRDHCLQYMTAVPLAFGNLVAEQYEDEfHAAHPIID 388
                                         *****************************************************************999******* PP

                           TIGR02330 363 elreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfs 437
                                         +lr+k+++ved+rysreyleadkrsianav+vffkdgs te+v+veyp+ghrrrr egip+l dkfkanlat+f+
  lcl|FitnessBrowser__WCS417:GFF4111 389 QLRDKMVIVEDPRYSREYLEADKRSIANAVQVFFKDGSCTEQVAVEYPIGHRRRRVEGIPLLEDKFKANLATRFT 463
                                         *************************************************************************** PP

                           TIGR02330 438 skkqerilelcldqakleatpvnefldlfvi 468
                                          ++ ++i+ lc dqa+leatpvn+f+dlfvi
  lcl|FitnessBrowser__WCS417:GFF4111 464 GQRSAEIFALCKDQARLEATPVNRFVDLFVI 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.60
//
[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