Alignments for a candidate for edd in Sinorhizobium meliloti 1021

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.2436.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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.34
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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