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.32638.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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.03
//
[ok]

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

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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