Alignments for a candidate for edd in Photobacterium gaetbulicola Gung47

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Photobacterium gaetbulicola Gung47

Align phosphogluconate dehydratase (characterized)
to candidate WP_044621646.1 H744_RS07730 phosphogluconate dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>NCBI__GCF_000940995.1:WP_044621646.1
          Length = 598

 Score =  612 bits (1577), Expect = e-179
 Identities = 311/599 (51%), Positives = 419/599 (69%), Gaps = 5/599 (0%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           ++P +  +T RI  RS+  RS++ A+I Q       R+ L+CGNLAH  AA   +DK  +
Sbjct: 2   IHPTITLITERIKARSQAHRSSFEAKITQQAEQGKGRTSLSCGNLAHAVAASCQQDKQQI 61

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
               R N+AI++SYNDMLSAHQ Y++YP+ I+ AL       Q+AG VPAMCDGVTQGQ 
Sbjct: 62  LDFTRANLAIVSSYNDMLSAHQLYKNYPDQIKSALQSLGHTAQIAGCVPAMCDGVTQGQP 121

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GM++SL SR++IA + A  LSHN+FD  L LG+CDKI PG  M ALS+ HLP  F+P+GP
Sbjct: 122 GMDMSLFSRDLIAQATAFSLSHNVFDATLLLGICDKIAPGQLMGALSYAHLPTAFIPAGP 181

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           M +G+ N +KV +RQ Y  G+V + ALLE E  +YH+ GTCTFYGTANTNQ+V E MG+ 
Sbjct: 182 MPTGITNDKKVAVRQQYVAGEVGKDALLEMECQAYHSGGTCTFYGTANTNQLVFEAMGLM 241

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGS+FV P++ LR ALT  A+  +  MT +   + P+  +   + +VNG+VALLA+GGS
Sbjct: 242 LPGSAFVAPNTDLRSALTEHASLALASMTADSPNYRPLIDVFTAENLVNGVVALLASGGS 301

Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360
           TNHT+H++A+ARA G+ + WDD S+LSD+VPL+A++YPNGPADIN F+ AGGVP L++ L
Sbjct: 302 TNHTIHMLAIARAGGLVLTWDDISELSDIVPLLAKMYPNGPADINAFEQAGGVPALMKTL 361

Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420
            + GLL+ DV TV G    + T +P + + +L W+   E S ++ VIA+  + FS  GGT
Sbjct: 362 HERGLLNSDVKTVFGEFADQLT-QPAITDSKLVWQPVGE-SRNAEVIAANGKAFSQTGGT 419

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           KVL GNLG+AV+K SAV  E+Q IEAPA VF  QHDV  A++AG    DCV+VV H GP 
Sbjct: 420 KVLKGNLGQAVIKVSAVKQEHQFIEAPAKVFHCQHDVEAAYQAGEFTGDCVIVVSHNGPA 479

Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540
           ANGMPELHKLMP LG +     ++ALVTDGRLSGASGK+P+AIHV+PEA  GG +  + D
Sbjct: 480 ANGMPELHKLMPILGNIQKAGHQVALVTDGRLSGASGKIPAAIHVSPEALRGGAIGMIND 539

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGAT 599
           GDI++++  TG L + VD      R+P   D  AS++  GR++F  +RE +  A++GA+
Sbjct: 540 GDIVKLDCSTGLLEVAVD---FDQRQPVQLDTEASQITWGRDIFKVMRENVGAADEGAS 595


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: 966
Number of extensions: 39
Number of successful extensions: 5
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: 598
Length adjustment: 37
Effective length of query: 566
Effective length of database: 561
Effective search space:   317526
Effective search space used:   317526
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 WP_044621646.1 H744_RS07730 (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.1846430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-249  814.7   2.9   2.3e-249  814.6   2.9    1.0  1  NCBI__GCF_000940995.1:WP_044621646.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000940995.1:WP_044621646.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.6   2.9  2.3e-249  2.3e-249       1     600 [.       3     597 ..       3     598 .] 0.98

  Alignments for each domain:
  == domain 1  score: 814.6 bits;  conditional E-value: 2.3e-249
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h+ ++ iteri +rs++ r+++ +ki++ +++gk r++l+cgnlah+vaa  +++k+++   +r+nlai+++y
  NCBI__GCF_000940995.1:WP_044621646.1   3 HPTITLITERIKARSQAHRSSFEAKITQQAEQGKGRTSLSCGNLAHAVAASCQQDKQQILDFTRANLAIVSSY 75 
                                           678999******************************************************************* PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahq +k+ypd+ik+alq  + +aq+ag vpamcdGvtqG++Gm++sl+srd+ia +ta +lshn+fd+
  NCBI__GCF_000940995.1:WP_044621646.1  76 NDMLSAHQLYKNYPDQIKSALQSLGHTAQIAGCVPAMCDGVTQGQPGMDMSLFSRDLIAQATAFSLSHNVFDA 148
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           +l+lG+cdki pG l++als+ hlp+ f+paGpm++G++n++k++vrq++  G v++++ll+ e ++yh+ Gt
  NCBI__GCF_000940995.1:WP_044621646.1 149 TLLLGICDKIAPGQLMGALSYAHLPTAFIPAGPMPTGITNDKKVAVRQQYVAGEVGKDALLEMECQAYHSGGT 221
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtan+nq++ e mGl lpg++fv pnt+lr alt++a+  la++ta++ ++ pl ++ +   +vn++v+
  NCBI__GCF_000940995.1:WP_044621646.1 222 CTFYGTANTNQLVFEAMGLMLPGSAFVAPNTDLRSALTEHASLALASMTADSPNYRPLIDVFTAENLVNGVVA 294
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           lla+GGstnht+h++aiara G++l+wdd+selsd+vplla++ypnG ad+n+fe aGG++ l++ l ++Gll
  NCBI__GCF_000940995.1:WP_044621646.1 295 LLASGGSTNHTIHMLAIARAGGLVLTWDDISELSDIVPLLAKMYPNGPADINAFEQAGGVPALMKTLHERGLL 367
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavke 438
                                             dv+tv g+   + t +p ++d+kl++++   +s + +++++  k fs++GG+k+lkGnlG+avikvsavk+
  NCBI__GCF_000940995.1:WP_044621646.1 368 NSDVKTVFGEFADQLT-QPAITDSKLVWQPVG-ESRNAEVIAANGKAFSQTGGTKVLKGNLGQAVIKVSAVKQ 438
                                           *********9888776.6999*******9865.699************************************* PP

                             TIGR01196 439 esrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrl 511
                                           e++ ieapa+vf+ q+++ aa++age+ +d+v+vv ++Gp anGmpelhkl++ lG +q  g++valvtdGrl
  NCBI__GCF_000940995.1:WP_044621646.1 439 EHQFIEAPAKVFHCQHDVEAAYQAGEFTGDCVIVVSHNGPAANGMPELHKLMPILGNIQKAGHQVALVTDGRL 511
                                           ************************************************************************* PP

                             TIGR01196 512 sGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfa 584
                                           sGasGk+paaihv+peal gGa+  i+dGd+++ld+ +g lev vd   ++ r++ +ld e++++  Gr++f 
  NCBI__GCF_000940995.1:WP_044621646.1 512 SGASGKIPAAIHVSPEALRGGAIGMINDGDIVKLDCSTGLLEVAVD---FDQRQPVQLDTEASQITWGRDIFK 581
                                           ***************************************9999875...78999999**************** PP

                             TIGR01196 585 alrekvssaeeGassl 600
                                            +re+v++a+eGas l
  NCBI__GCF_000940995.1:WP_044621646.1 582 VMRENVGAADEGASFL 597
                                           ************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (598 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 38.99
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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