Alignments for a candidate for edd in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Shewanella sp. ANA-3

Align phosphogluconate dehydratase (characterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__ANA3:7024978
          Length = 608

 Score =  814 bits (2103), Expect = 0.0
 Identities = 406/598 (67%), Positives = 487/598 (81%)

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

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           + + + NI IIT++NDMLSAHQPYE YPE+++KA  E  +V QVAGGVPAMCDGVTQGQ 
Sbjct: 61  RQLTKANIGIITAFNDMLSAHQPYETYPELLKKACQEVGSVAQVAGGVPAMCDGVTQGQP 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 VVNGIVALLATGGS
Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGIVALLATGGS 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 AGLLHEDVNTVAGFGL RYT EP L +GEL W +G   SLD+ V+ S   PF ++GG 
Sbjct: 361 LDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGL 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           K+L GNLGRAV+K SAV  +++V+EAPAVV + Q+ +   F++G LDRDCVVVV+ QGPK
Sbjct: 421 KLLKGNLGRAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPK 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 +AELAAR     DL  SR G GRELF ALR  LS  E GA
Sbjct: 541 GDLIRVDALTGELSLLVSDAELAARTAAEIDLRHSRYGMGRELFGALRSNLSSPETGA 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: 1058
Number of extensions: 30
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 7024978 Shewana3_2149 (phosphogluconate dehydratase (RefSeq))
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.2142.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 1028.8   1.3          0 1028.6   1.3    1.0  1  lcl|FitnessBrowser__ANA3:7024978  Shewana3_2149 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024978  Shewana3_2149 phosphogluconate dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1028.6   1.3         0         0       1     599 [.       2     600 ..       2     602 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1028.6 bits;  conditional E-value: 0
                         TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndml 77 
                                       hs ++++t+rii+rsk+ re+yl+ +++a+++g++rs+l+cgnlahg+aa+s+++k +l++ +++n++iita+ndml
  lcl|FitnessBrowser__ANA3:7024978   2 HSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACSPDDKNSLRQLTKANIGIITAFNDML 78 
                                       678999*********************************************************************** PP

                         TIGR01196  78 sahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcd 154
                                       sahqp+++yp+l+kka+qe ++vaqvagGvpamcdGvtqG++Gmelsllsr+via++ta+glshnmfdgal+lG+cd
  lcl|FitnessBrowser__ANA3:7024978  79 SAHQPYETYPELLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICD 155
                                       ***************************************************************************** PP

                         TIGR01196 155 kivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqm 231
                                       kivpGlli+alsfGhlp +fvpaGpm sG++nkeka++rq+fa+Gkvdr +ll++e++syh++GtctfyGtansnq+
  lcl|FitnessBrowser__ANA3:7024978 156 KIVPGLLIGALSFGHLPMLFVPAGPMKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQL 232
                                       ***************************************************************************** PP

                         TIGR01196 232 lvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlva 308
                                       ++e+mGl+lpg+sfvnp+ plr+al + aak++ rlt  + ++ p++e+++eks+vn++v+llatGGstn t+h+va
  lcl|FitnessBrowser__ANA3:7024978 233 MLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGIVALLATGGSTNLTMHIVA 309
                                       ***************************************************************************** PP

                         TIGR01196 309 iaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepf 385
                                        araaGii+nwdd+selsd vpllarvypnG+ad+nhf+aaGG++fli+ell++Gllhedv+tvag Glrryt+ep+
  lcl|FitnessBrowser__ANA3:7024978 310 AARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKELLDAGLLHEDVNTVAGFGLRRYTQEPK 386
                                       ***************************************************************************** PP

                         TIGR01196 386 ledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafka 462
                                       l dg+l++ +++  sld+++l +v +pf+++GGlkllkGnlGravikvsav+e++rv+eapa+v +dq++l a fk+
  lcl|FitnessBrowser__ANA3:7024978 387 LLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKS 463
                                       ***************************************************************************** PP

                         TIGR01196 463 gelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakird 539
                                       g l+rd+v+vv+ qGpkanGmpelhklt+ lG lqd+gfkval+tdGr+sGasGkvpaaih+tpea++gG +ak++d
  lcl|FitnessBrowser__ANA3:7024978 464 GALDRDCVVVVKGQGPKANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQD 540
                                       ***************************************************************************** PP

                         TIGR01196 540 GdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599
                                       Gdlir+da +gel++lv dael+ar+ +e+dl ++++G+Grelf alr+++ss e+Ga s
  lcl|FitnessBrowser__ANA3:7024978 541 GDLIRVDALTGELSLLVSDAELAARTAAEIDLRHSRYGMGRELFGALRSNLSSPETGARS 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: 7.56
//
[ok]

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

Downloads

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

Related tools

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