Alignments for a candidate for edd in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Shewanella oneidensis MR-1

Align phosphogluconate dehydratase (characterized)
to candidate 201628 SO2487 6-phosphogluconate dehydratase (NCBI ptt file)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__MR1:201628
          Length = 608

 Score =  806 bits (2082), Expect = 0.0
 Identities = 399/598 (66%), Positives = 484/598 (80%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           M+  +  VT+RII RS+ +R AYLA +  A+   VHRS L+CGNLAHGFAAC P+DK +L
Sbjct: 1   MHSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACNPDDKNAL 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           + + + NI IIT++NDMLSAHQPYE YP++++KA  E  +V QVAGGVPAMCDGVTQGQ 
Sbjct: 61  RQLTKANIGIITAFNDMLSAHQPYETYPDLLKKACQEVGSVAQVAGGVPAMCDGVTQGQP 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAM+ AVGLSHNMFDGAL LG+CDKIVPGL + ALSFGHLP +FVP+GP
Sbjct: 121 GMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           M SG+PNKEK RIRQ +A+GKVDR  LLE+EA SYH+ GTCTFYGTAN+NQ+++E MG+Q
Sbjct: 181 MKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGLQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFV+PD PLR+AL   AA+QV R+T  G ++ PIG++++EK +VNGIVALLATGGS
Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGS 300

Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360
           TN TMH+VA ARAAGI +NWDDFS+LSD VPL+AR+YPNG ADINHF AAGG+  L++EL
Sbjct: 301 TNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKEL 360

Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420
           L AGLLHEDVNTVAG+GL RYT EP L +GEL W +G   SLD+ V+ S   PF ++GG 
Sbjct: 361 LDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGL 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           K+L GNLGRAV+K SAV  +++V+EAPAVV + Q+ +   F++G LDRDCVVVV+ QGPK
Sbjct: 421 KLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPK 480

Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540
           ANGMPELHKL P LG L D+ FK+AL+TDGR+SGASGKVP+AIH+TPEA DGGL+AKV+D
Sbjct: 481 ANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQD 540

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGA 598
           GD+IRV+  TGEL+LLV + ELA R     DL  SR G GRELF  LR  LS  E GA
Sbjct: 541 GDLIRVDALTGELSLLVSDTELATRTATEIDLRHSRYGMGRELFGVLRSNLSSPETGA 598


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: 1061
Number of extensions: 31
Number of successful extensions: 1
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: 608
Length adjustment: 37
Effective length of query: 566
Effective length of database: 571
Effective search space:   323186
Effective search space used:   323186
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 201628 SO2487 (6-phosphogluconate dehydratase (NCBI ptt file))
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.5632.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 1027.7   0.9          0 1027.5   0.9    1.0  1  lcl|FitnessBrowser__MR1:201628  SO2487 6-phosphogluconate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201628  SO2487 6-phosphogluconate dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1027.5   0.9         0         0       1     599 [.       2     600 ..       2     602 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1027.5 bits;  conditional E-value: 0
                       TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmlsa 79 
                                     hs ++++t+rii+rsk+ re+yl+ +++a+++g++rs+l+cgnlahg+aa+++++k +l++ +++n++iita+ndmlsa
  lcl|FitnessBrowser__MR1:201628   2 HSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACNPDDKNALRQLTKANIGIITAFNDMLSA 80 
                                     678999************************************************************************* PP

                       TIGR01196  80 hqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkivp 158
                                     hqp+++ypdl+kka+qe ++vaqvagGvpamcdGvtqG++Gmelsllsr+via++ta+glshnmfdgal+lG+cdkivp
  lcl|FitnessBrowser__MR1:201628  81 HQPYETYPDLLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVP 159
                                     ******************************************************************************* PP

                       TIGR01196 159 GlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmG 237
                                     Glli+alsfGhlp +fvpaGpm sG++nkeka++rq+fa+Gkvdr +ll++e++syh++GtctfyGtansnq+++e+mG
  lcl|FitnessBrowser__MR1:201628 160 GLLIGALSFGHLPMLFVPAGPMKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMG 238
                                     ******************************************************************************* PP

                       TIGR01196 238 lhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGii 316
                                     l+lpg+sfvnp+ plr+al + aak++ rlt  + ++ p++e+++eksivn++v+llatGGstn t+h+va araaGii
  lcl|FitnessBrowser__MR1:201628 239 LQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGSTNLTMHIVAAARAAGII 317
                                     ******************************************************************************* PP

                       TIGR01196 317 lnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyre 395
                                     +nwdd+selsd vpllarvypnG+ad+nhf+aaGG++fli+ell++Gllhedv+tvag Glrryt+ep+l dg+l++ +
  lcl|FitnessBrowser__MR1:201628 318 VNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKELLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVD 396
                                     ******************************************************************************* PP

                       TIGR01196 396 aaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvr 474
                                     ++  sld+++l +v +pf+++GGlkllkGnlGravikvsav++++rv+eapa+v +dq++l a fk+g l+rd+v+vv+
  lcl|FitnessBrowser__MR1:201628 397 GPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVK 475
                                     ******************************************************************************* PP

                       TIGR01196 475 fqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngele 553
                                      qGpkanGmpelhklt+ lG lqd+gfkval+tdGr+sGasGkvpaaih+tpea++gG +ak++dGdlir+da +gel+
  lcl|FitnessBrowser__MR1:201628 476 GQGPKANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQDGDLIRVDALTGELS 554
                                     ******************************************************************************* PP

                       TIGR01196 554 vlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599
                                     +lv d+el++r+ +e+dl ++++G+Grelf  lr+++ss e+Ga s
  lcl|FitnessBrowser__MR1:201628 555 LLVSDTELATRTATEIDLRHSRYGMGRELFGVLRSNLSSPETGARS 600
                                     *******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.00
//
[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