Alignments for a candidate for edd in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Shewanella loihica PV-4

Align phosphogluconate dehydratase (characterized)
to candidate 5209582 Shew_2046 phosphogluconate dehydratase (RefSeq)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__PV4:5209582
          Length = 608

 Score =  805 bits (2079), Expect = 0.0
 Identities = 399/602 (66%), Positives = 486/602 (80%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           M+  +  VT+RII RS+ TR+ YLA + +AK + VHRS L+CGNLAHGFAAC P DK ++
Sbjct: 1   MHSVVQSVTDRIIARSQATRAKYLAALGEAKANGVHRSSLSCGNLAHGFAACSPADKNAI 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           K+  + NI I+T++NDMLSAHQPYEHYP++++ A HE  +V QVA GVPAMCDGVTQGQ 
Sbjct: 61  KAFNKANIGIVTAFNDMLSAHQPYEHYPQLLKDACHEVGSVAQVAAGVPAMCDGVTQGQP 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAMS AVGLSHNMFDGAL LG+CDKIVPGL + ALSFGHLP +FVP+GP
Sbjct: 121 GMELSLLSREVIAMSTAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           M SG+PNKEK R+RQ +A+G+VDR ALLE+E+ SYH+ GTCTFYGTAN+NQ+++E MG+Q
Sbjct: 181 MKSGIPNKEKARVRQKFAQGQVDRAALLEAESKSYHSAGTCTFYGTANSNQLMLEVMGLQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFV+PD PLR+AL   AA+QV R+T  G ++ PIG++++EK VVNGIVALLATGGS
Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGS 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 AGLLHEDV TVAG GL RYT EP L + EL W EG  +SLD  V+ +   PF  +GG 
Sbjct: 361 LDAGLLHEDVLTVAGPGLRRYTQEPRLIDNELVWVEGPNESLDKEVLTAVASPFQANGGL 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           K+L GNLGRAV+K SAV   ++ +EAPAVV + Q+ +   F+AG LDRDCVVVV+ QGPK
Sbjct: 421 KLLKGNLGRAVIKVSAVAESHRFVEAPAVVIDDQNKLEGLFKAGELDRDCVVVVKGQGPK 480

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

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600
           GD+IRV+  TGE++LLVDEA LA+RE    DL ++  G GRELF+ALR  LS  E GA C
Sbjct: 541 GDLIRVDANTGEVSLLVDEAVLASREVEKVDLRSTSFGMGRELFAALRSNLSSPETGARC 600

Query: 601 IT 602
            T
Sbjct: 601 TT 602


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: 1067
Number of extensions: 34
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 5209582 Shew_2046 (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.32593.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 1020.3   2.4          0 1020.0   2.4    1.0  1  lcl|FitnessBrowser__PV4:5209582  Shew_2046 phosphogluconate dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209582  Shew_2046 phosphogluconate dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1020.0   2.4         0         0       1     600 [.       2     601 ..       2     602 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1020.0 bits;  conditional E-value: 0
                        TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmls 78 
                                      hs ++++t+rii+rs++tr kyl+ + +ak +g++rs+l+cgnlahg+aa+s+++k ++k  +++n++i+ta+ndmls
  lcl|FitnessBrowser__PV4:5209582   2 HSVVQSVTDRIIARSQATRAKYLAALGEAKANGVHRSSLSCGNLAHGFAACSPADKNAIKAFNKANIGIVTAFNDMLS 79 
                                      678999************************************************************************ PP

                        TIGR01196  79 ahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdki 156
                                      ahqp+++yp+l+k+a++e ++vaqva+GvpamcdGvtqG++Gmelsllsr+via+sta+glshnmfdgal+lG+cdki
  lcl|FitnessBrowser__PV4:5209582  80 AHQPYEHYPQLLKDACHEVGSVAQVAAGVPAMCDGVTQGQPGMELSLLSREVIAMSTAVGLSHNMFDGALLLGICDKI 157
                                      ****************************************************************************** PP

                        TIGR01196 157 vpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlve 234
                                      vpGlli+alsfGhlp +fvpaGpm sG++nkeka+vrq fa+G+vdr +ll++e++syh++GtctfyGtansnq+++e
  lcl|FitnessBrowser__PV4:5209582 158 VPGLLIGALSFGHLPMLFVPAGPMKSGIPNKEKARVRQKFAQGQVDRAALLEAESKSYHSAGTCTFYGTANSNQLMLE 235
                                      ****************************************************************************** PP

                        TIGR01196 235 lmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiara 312
                                      +mGl+lpg+sfvnp+ plr+al + aak++ rlt  + +++p++e+++eks+vn++v+llatGGstn t+h+va ara
  lcl|FitnessBrowser__PV4:5209582 236 VMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGSTNLTMHIVAAARA 313
                                      ****************************************************************************** PP

                        TIGR01196 313 aGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgk 390
                                      aGii+nwdd+selsd vpllarvypnG+ad+nhf+aaGG++fli+ell++Gllhedv tvag Glrryt+ep l d++
  lcl|FitnessBrowser__PV4:5209582 314 AGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKELLDAGLLHEDVLTVAGPGLRRYTQEPRLIDNE 391
                                      ****************************************************************************** PP

                        TIGR01196 391 leyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerd 468
                                      l++ e++++sld+++l +v +pf+a+GGlkllkGnlGravikvsav+e +r +eapa+v +dq++l   fkagel+rd
  lcl|FitnessBrowser__PV4:5209582 392 LVWVEGPNESLDKEVLTAVASPFQANGGLKLLKGNLGRAVIKVSAVAESHRFVEAPAVVIDDQNKLEGLFKAGELDRD 469
                                      ****************************************************************************** PP

                        TIGR01196 469 lvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirld 546
                                      +v+vv+ qGpkanGmpelhklt+ lG lqd+gfkval+tdGr+sGasGkvpaaih+tpeal+gG +ak+++Gdlir+d
  lcl|FitnessBrowser__PV4:5209582 470 CVVVVKGQGPKANGMPELHKLTPILGSLQDKGFKVALLTDGRMSGASGKVPAAIHLTPEALDGGLIAKVENGDLIRVD 547
                                      ****************************************************************************** PP

                        TIGR01196 547 avngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                      a +ge+++lvd+a l++re+e++dl ++++G+Grelfaalr+++ss e+Ga + 
  lcl|FitnessBrowser__PV4:5209582 548 ANTGEVSLLVDEAVLASREVEKVDLRSTSFGMGRELFAALRSNLSSPETGARCT 601
                                      **************************************************9875 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.79
//
[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