GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Sinorhizobium meliloti 1021

Align phosphogluconate dehydratase (characterized)
to candidate SMc03068 SMc03068 phosphogluconate dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__Smeli:SMc03068
          Length = 606

 Score =  728 bits (1878), Expect = 0.0
 Identities = 357/599 (59%), Positives = 456/599 (76%), Gaps = 1/599 (0%)

Query: 4   QLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASLKSM 63
           ++  +T RI+ERS+  R  YL R+  A T+  HR+ L CGNLAHGFA C P +K +L   
Sbjct: 6   RIAAITARIVERSKPYREPYLDRVRSAATNGPHRTVLGCGNLAHGFAVCSPAEKVALAGD 65

Query: 64  LRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGME 123
              N+ IITSYNDMLSAHQP+E YP +IR+A HEA  V QVAGGVPAMCDGVTQGQ GME
Sbjct: 66  RVPNLGIITSYNDMLSAHQPFETYPALIREAAHEAGGVAQVAGGVPAMCDGVTQGQPGME 125

Query: 124 LSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMAS 183
           LSL SR+VIAM+A +GLSHNMFD A++LGVCDKIVPGL +AAL+FGHLPAVF+P+GPM +
Sbjct: 126 LSLFSRDVIAMAAGIGLSHNMFDAAVYLGVCDKIVPGLAIAALTFGHLPAVFIPAGPMTT 185

Query: 184 GLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPG 243
           GLPN EK ++RQL+AEGKV R  LLE+E+ SYH PGTCTFYGTAN+NQM++E MG  LPG
Sbjct: 186 GLPNDEKAKVRQLFAEGKVGRDELLEAESKSYHGPGTCTFYGTANSNQMLMEIMGFHLPG 245

Query: 244 SSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNH 303
           +SF++P +PLRDALT  A ++   +T  GNE+ P G+MIDE+ +VNG+V L ATGGSTNH
Sbjct: 246 ASFINPGTPLRDALTREATKRALAITALGNEFTPAGEMIDERSIVNGVVGLHATGGSTNH 305

Query: 304 TMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKA 363
           TMHLVAMARAAGI + W D S+LSD+VPL+AR+YPNG AD+NHF AAGG+  L+ +LL+ 
Sbjct: 306 TMHLVAMARAAGIVLTWQDISELSDLVPLLARVYPNGLADVNHFHAAGGMGFLIAQLLRK 365

Query: 364 GLLHEDVNTVAGFGLSRYTLEPWL-NNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKV 422
           GLLH+DV TV G GLS Y ++  L  NG +      E S D  V+A+ ++PF H GG K+
Sbjct: 366 GLLHDDVRTVYGQGLSAYAIDVKLGENGSVKREPAPEASADPKVLATVDRPFQHTGGLKM 425

Query: 423 LSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPKAN 482
           LSGN+G+AV+K SAV  E+ VIEAPA +F  Q ++  AF+AG L+ D V VVR QGPKAN
Sbjct: 426 LSGNIGKAVIKISAVKPESHVIEAPAKIFNDQAELNAAFKAGKLEGDFVAVVRFQGPKAN 485

Query: 483 GMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGD 542
           GMPELHKL   LG+L DR  K+A++TDGR+SGASGKVP+AIHVTPEA +GG +A++++GD
Sbjct: 486 GMPELHKLTTVLGILQDRGQKVAILTDGRMSGASGKVPAAIHVTPEAKEGGPIARIQEGD 545

Query: 543 IIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATCI 601
           I+R++   G++ +LV++  L  R P   DLS +  G GRELF+  R+    A++G + +
Sbjct: 546 IVRIDAINGKVEVLVEDIALKTRVPAHIDLSDNEFGMGRELFAPFRQIAGAADRGGSVL 604


Lambda     K      H
   0.318    0.134    0.392 

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: 1127
Number of extensions: 58
Number of successful extensions: 2
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: 603
Length of database: 606
Length adjustment: 37
Effective length of query: 566
Effective length of database: 569
Effective search space:   322054
Effective search space used:   322054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate SMc03068 SMc03068 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

# 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/TIGR01196.hmm
# target sequence database:        /tmp/gapView.27741.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01196  [M=601]
Accession:   TIGR01196
Description: edd: phosphogluconate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1115.2   0.6          0 1115.0   0.6    1.0  1  lcl|FitnessBrowser__Smeli:SMc03068  SMc03068 phosphogluconate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03068  SMc03068 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1115.0   0.6         0         0       1     600 [.       4     604 ..       4     605 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1115.0 bits;  conditional E-value: 0
                           TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                         +sr+a+it+ri+ersk++re yl+++rsa+t+g++r++lgcgnlahg+a++s++ekv+l+ ++++nl+iit+ynd
  lcl|FitnessBrowser__Smeli:SMc03068   4 DSRIAAITARIVERSKPYREPYLDRVRSAATNGPHRTVLGCGNLAHGFAVCSPAEKVALAGDRVPNLGIITSYND 78 
                                         699************************************************************************ PP

                           TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150
                                         mlsahqpf++yp+li++a++ea++vaqvagGvpamcdGvtqG++Gmelsl+srdvia++++iglshnmfd+a++l
  lcl|FitnessBrowser__Smeli:SMc03068  79 MLSAHQPFETYPALIREAAHEAGGVAQVAGGVPAMCDGVTQGQPGMELSLFSRDVIAMAAGIGLSHNMFDAAVYL 153
                                         *************************************************************************** PP

                           TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225
                                         GvcdkivpGl+iaal+fGhlpavf+paGpm++Gl+n+ekakvrqlfaeGkv+r+ell++e++syh+pGtctfyGt
  lcl|FitnessBrowser__Smeli:SMc03068 154 GVCDKIVPGLAIAALTFGHLPAVFIPAGPMTTGLPNDEKAKVRQLFAEGKVGRDELLEAESKSYHGPGTCTFYGT 228
                                         *************************************************************************** PP

                           TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300
                                         ansnqml+e+mG+hlpgasf+np tplrdaltrea+kr+ ++ta ++e++p++e+ide+sivn++vgl+atGGst
  lcl|FitnessBrowser__Smeli:SMc03068 229 ANSNQMLMEIMGFHLPGASFINPGTPLRDALTREATKRALAITALGNEFTPAGEMIDERSIVNGVVGLHATGGST 303
                                         *************************************************************************** PP

                           TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375
                                         nht+hlva+araaGi+l+w+d+selsdlvpllarvypnG advnhf+aaGG++fli++ll++Gllh+dv+tv+g+
  lcl|FitnessBrowser__Smeli:SMc03068 304 NHTMHLVAMARAAGIVLTWQDISELSDLVPLLARVYPNGLADVNHFHAAGGMGFLIAQLLRKGLLHDDVRTVYGQ 378
                                         *************************************************************************** PP

                           TIGR01196 376 Glrrytkepfled.gkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaiv 449
                                         Gl++y+++++l + g++++++a+e+s+d ++l++vd+pf+++GGlk+l+Gn+G+avik+savk+es+vieapa++
  lcl|FitnessBrowser__Smeli:SMc03068 379 GLSAYAIDVKLGEnGSVKREPAPEASADPKVLATVDRPFQHTGGLKMLSGNIGKAVIKISAVKPESHVIEAPAKI 453
                                         ***********7659************************************************************ PP

                           TIGR01196 450 fkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihv 524
                                         f+dqael+aafkag+le+d+vavvrfqGpkanGmpelhklttvlG+lqdrg+kva++tdGr+sGasGkvpaaihv
  lcl|FitnessBrowser__Smeli:SMc03068 454 FNDQAELNAAFKAGKLEGDFVAVVRFQGPKANGMPELHKLTTVLGILQDRGQKVAILTDGRMSGASGKVPAAIHV 528
                                         *************************************************************************** PP

                           TIGR01196 525 tpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599
                                         tpea+egG++a+i++Gd++r+da+ng++evlv+d++lk+r+++++dl+dne+G+Grelfa +r+++++a++G+s+
  lcl|FitnessBrowser__Smeli:SMc03068 529 TPEAKEGGPIARIQEGDIVRIDAINGKVEVLVEDIALKTRVPAHIDLSDNEFGMGRELFAPFRQIAGAADRGGSV 603
                                         *************************************************************************98 PP

                           TIGR01196 600 l 600
                                         l
  lcl|FitnessBrowser__Smeli:SMc03068 604 L 604
                                         7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (606 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: 10.99
//
[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