GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Pseudomonas fluorescens FW300-N2E3

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate AO353_00880 AO353_00880 2-methylcitrate dehydratase

Query= BRENDA::P74840
         (483 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_00880
          Length = 494

 Score =  600 bits (1547), Expect = e-176
 Identities = 306/492 (62%), Positives = 370/492 (75%), Gaps = 16/492 (3%)

Query: 5   ELNIRPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPI 64
           +LNIRPD+D+ + DI DYV+N++I SK A DTA  CL+DTLGCGL AL +P C K LGPI
Sbjct: 6   DLNIRPDYDKVLQDIADYVLNFKIESKEALDTARNCLMDTLGCGLLALRFPECTKHLGPI 65

Query: 65  VPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATA 124
           V GTVVP GARVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGGILA A
Sbjct: 66  VEGTVVPFGARVPGTHFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVA 125

Query: 125 DWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVASTAVVA 184
           D LS+  VA G APLTM+ VL  MI AHEIQG IALEN+FNRVGLDHVLLVKVASTAV A
Sbjct: 126 DHLSQKRVANGDAPLTMRAVLDAMIMAHEIQGVIALENSFNRVGLDHVLLVKVASTAVTA 185

Query: 185 EMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEM 244
           +++G  R+++L A+S A+VDGQ+LRTYRHAPN G+RKSWAAGDA+SR VRLA +A  GEM
Sbjct: 186 KLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEM 245

Query: 245 GYPSALTAKTWGFYDVSFK------------GETFRFQRPYGSYVMENVLFKISFPAEFH 292
           G P  LTA  WGFYDV F               TF   + YG+YVMENVLFKISFPAEFH
Sbjct: 246 GIPGVLTAPQWGFYDVLFSHTNKDLALKPADKRTFSLSQKYGTYVMENVLFKISFPAEFH 305

Query: 293 SQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMV 352
           +QTA EAA+TL+ Q+        +I+K+ I THE+ +RII K G L N ADRDHCIQYM 
Sbjct: 306 AQTACEAAVTLHPQV---SNRLDEIDKIVITTHESAIRIISKVGQLANAADRDHCIQYMT 362

Query: 353 AVPLLFGRLTAADYEDEV-AQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEF 411
           AVPL FG L A  YED+  A    ID LR+K+V  EDP +T +Y + +KR+I NA+ V F
Sbjct: 363 AVPLAFGTLVAEQYEDQFHAAHPIIDELRKKMVIVEDPRYTREYLEADKRSIANALQVFF 422

Query: 412 TDGSRFGEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQ 471
            DGS  G+VVVEYPIGH RRRA+GIP L +KFK NLA +F  ++  +I  +  D+A+LE 
Sbjct: 423 KDGSSTGQVVVEYPIGHRRRRAEGIPLLEDKFKANLATRFTAQRSAQIFALCQDQAKLEA 482

Query: 472 MPVNEYLDLYVI 483
            PVN ++DL+VI
Sbjct: 483 TPVNRFMDLFVI 494


Lambda     K      H
   0.321    0.136    0.408 

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: 658
Number of extensions: 20
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
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 AO353_00880 AO353_00880 (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.15553.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   6.6e-272  888.0   0.1   7.5e-272  887.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  AO353_00880 2-methylcitrate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  AO353_00880 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.8   0.1  7.5e-272  7.5e-272       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 887.8 bits;  conditional E-value: 7.5e-272
                                     TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvp 65 
                                                   d+vl+diadyvl+++i+skea+dtar++l+dtlgcgllal++pectk+lgp+vegt+vp garvp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  14 DKVLQDIADYVLNFKIESKEALDTARNCLMDTLGCGLLALRFPECTKHLGPIVEGTVVPFGARVP 78 
                                                   89*************************************************************** PP

                                     TIGR02330  66 gtsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvk 130
                                                   gt+++ldpvkaa++ig++vrwldyndtwlaaewghpsdnlggilavad+ls+kr+a+g++pl+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  79 GTHFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQKRVANGDAPLTMR 143
                                                   ***************************************************************** PP

                                     TIGR02330 131 evleamikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqa 195
                                                    vl+ami+aheiqgv+alensfnrvgldhvllvkvastav+akl+ga+re++l+alshafvdgqa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 144 AVLDAMIMAHEIQGVIALENSFNRVGLDHVLLVKVASTAVTAKLMGANREQLLAALSHAFVDGQA 208
                                                   ***************************************************************** PP

                                     TIGR02330 196 lrtyrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkke....... 253
                                                   lrtyrhapn+gsrkswaagda+srgvrla+ia++gemg+p++l+ap+wgf+dvlf+++       
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 209 LRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEMGIPGVLTAPQWGFYDVLFSHTnkdlalk 273
                                                   *********************************************************99****** PP

                                     TIGR02330 254 .....klklareygsyvmenvlfkisfpaefhaqtaveaavklheevkerldeierivitthesa 313
                                                         ++l+++yg+yvmenvlfkisfpaefhaqta+eaav+lh++v +rldei++ivitthesa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 274 padkrTFSLSQKYGTYVMENVLFKISFPAEFHAQTACEAAVTLHPQVSNRLDEIDKIVITTHESA 338
                                                   ****99*********************************************************** PP

                                     TIGR02330 314 iriidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadpridelreklevvedkrys 377
                                                   irii+k+g lan adrdhc+qy++avpl fg lvae+yed+ +aa+p idelr+k+++ved+ry+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 339 IRIISKVGQLANAADRDHCIQYMTAVPLAFGTLVAEQYEDQfHAAHPIIDELRKKMVIVEDPRYT 403
                                                   *****************************************99********************** PP

                                     TIGR02330 378 reyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfsskkqe 442
                                                   reyleadkrsiana++vffkdgs+t++v+veyp+ghrrrr+egip+l dkfkanlat+f++++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 404 REYLEADKRSIANALQVFFKDGSSTGQVVVEYPIGHRRRRAEGIPLLEDKFKANLATRFTAQRSA 468
                                                   ***************************************************************** PP

                                     TIGR02330 443 rilelcldqakleatpvnefldlfvi 468
                                                   +i+ lc dqakleatpvn+f+dlfvi
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 469 QIFALCQDQAKLEATPVNRFMDLFVI 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: 12.66
//
[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:

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