Alignments for a candidate for edd in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Sphingomonas koreensis DSMZ 15582

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate Ga0059261_0354 Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12)

Query= SwissProt::P21909
         (607 letters)



>FitnessBrowser__Korea:Ga0059261_0354
          Length = 608

 Score =  777 bits (2007), Expect = 0.0
 Identities = 383/607 (63%), Positives = 474/607 (78%), Gaps = 3/607 (0%)

Query: 1   MTDLHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVD-RPNLSCSNLAHGFAAMNGDK 59
           +T+L   +  VT R+IERS++ R AY  L+  +RE G   R  L C+NLAH +A  +  +
Sbjct: 1   VTNLLPEIAAVTDRIIERSKKRRAAYNALMTAQREAGSSSRGRLGCANLAHAYAGTDEQR 60

Query: 60  PALRDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQ 119
             ++  NRMNIG+VT+YNDMLSAH PYYRYPEQMK++A E GAT QVAGGVPAMCDGVTQ
Sbjct: 61  DVMKPANRMNIGIVTAYNDMLSAHAPYYRYPEQMKIWALEAGATAQVAGGVPAMCDGVTQ 120

Query: 120 GQPGMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVP 179
           G  GME SLFSRD IA++T+V+LSH  FEGAALLGICDKIVPGLLMGALRFGHLP +L+P
Sbjct: 121 GYAGMELSLFSRDTIAMSTAVALSHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIP 180

Query: 180 SGPMTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVL 239
            G M TGI NKEK R+R+LYA+GK  ++ELLD E A YH +GTCTFYGTAN+NQM++E +
Sbjct: 181 GGAMPTGIANKEKARVRELYAEGKASREELLDSEIAAYHGKGTCTFYGTANSNQMMVEAM 240

Query: 240 GLHMPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLAT 299
           GLHMPG+AF+ PGT LRQALTRAAV R+ E+GW  +DYRP+G+I+DE++IVNA V LLAT
Sbjct: 241 GLHMPGAAFIHPGTKLRQALTRAAVQRLPEIGWDSNDYRPIGEIVDERAIVNAAVVLLAT 300

Query: 300 GGSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVI 359
           GGSTNH +H+PAIAR AGV+++W+DF  LS VVPL+AR+YPNG  D+N F++AGG  +VI
Sbjct: 301 GGSTNHLIHLPAIARCAGVLIDWDDFDRLSRVVPLLARVYPNGSADVNGFEDAGGPTFVI 360

Query: 360 KELLSANLLNRDVTTIAKGGIEEYAKAPALNDAGELVWKPAG-EPGDDTILRPVSNPFAK 418
           +EL+   +L+ D  T+A   + +Y + P L D   LVWK  G + GDD+ILR +  PF++
Sbjct: 361 RELIKGGVLHGDTLTVAGDSLADYVRRPVLED-DTLVWKDHGAKSGDDSILRTIDAPFSE 419

Query: 419 DGGLRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRF 478
           +GG R+L GNLGRA  K SAV+   WTIEAP RVF+ Q +VQ AFKAGEL++DV+VVVRF
Sbjct: 420 EGGFRILSGNLGRACIKVSAVERDRWTIEAPCRVFATQQEVQDAFKAGELDRDVVVVVRF 479

Query: 479 QGPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIG 538
           QGPRANGMPELHKLTP LGVLQ+ G++VALVTDGRMSGA+GKVP A+H+SPEA+GGG IG
Sbjct: 480 QGPRANGMPELHKLTPPLGVLQNKGFRVALVTDGRMSGASGKVPAAIHLSPEAIGGGPIG 539

Query: 539 KLRDGDIVRISVEEGKLEALVPADEWNARPHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598
           KLRDGD+VR+  EEG L+ALV   EW AR  A  P    GTGRELF + R  A++AE G 
Sbjct: 540 KLRDGDVVRLCAEEGILQALVEPAEWEARELAAAPPPDLGTGRELFAMMRAGASEAEAGG 599

Query: 599 VAIYAGA 605
            A+ A A
Sbjct: 600 SAMLAAA 606


Lambda     K      H
   0.318    0.136    0.403 

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: 1161
Number of extensions: 46
Number of successful extensions: 2
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: 607
Length of database: 608
Length adjustment: 37
Effective length of query: 570
Effective length of database: 571
Effective search space:   325470
Effective search space used:   325470
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 Ga0059261_0354 Ga0059261_0354 (6-phosphogluconate dehydratase (EC 4.2.1.12))
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.26928.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-274  896.1   0.0   5.5e-274  895.9   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0354  Ga0059261_0354 6-phosphogluconat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0354  Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  895.9   0.0  5.5e-274  5.5e-274       3     600 ..       7     602 ..       5     603 .. 0.98

  Alignments for each domain:
  == domain 1  score: 895.9 bits;  conditional E-value: 5.5e-274
                                 TIGR01196   3 rlaeiteriierskktrekylekirsaktkgk.lrstlgcgnlahgvaalsesekvelksekrknlaii 70 
                                               ++a++t+riierskk r +y + +++ ++ g   r++lgc+nlah++a  +e+ +  +k  +r n++i+
  lcl|FitnessBrowser__Korea:Ga0059261_0354   7 EIAAVTDRIIERSKKRRAAYNALMTAQREAGSsSRGRLGCANLAHAYAGTDEQ-RDVMKPANRMNIGIV 74 
                                               7899****************99998888777516778***********98766.567999********* PP

                                 TIGR01196  71 tayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaigl 139
                                               tayndmlsah p+ +yp+++k  + ea+a+aqvagGvpamcdGvtqG++Gmelsl+srd ia+sta++l
  lcl|FitnessBrowser__Korea:Ga0059261_0354  75 TAYNDMLSAHAPYYRYPEQMKIWALEAGATAQVAGGVPAMCDGVTQGYAGMELSLFSRDTIAMSTAVAL 143
                                               ********************************************************************* PP

                                 TIGR01196 140 shnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellk 208
                                               shn f+ga +lG+cdkivpGll++al fGhlp v++p+G m++G+ nkeka+vr+l+aeGk++reell+
  lcl|FitnessBrowser__Korea:Ga0059261_0354 144 SHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIPGGAMPTGIANKEKARVRELYAEGKASREELLD 212
                                               ********************************************************************* PP

                                 TIGR01196 209 semasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlpl 277
                                               se+a+yh+ GtctfyGtansnqm+ve mGlh+pga+f++p t+lr+altr+a +rl ++  +++++ p+
  lcl|FitnessBrowser__Korea:Ga0059261_0354 213 SEIAAYHGKGTCTFYGTANSNQMMVEAMGLHMPGAAFIHPGTKLRQALTRAAVQRLPEIGWDSNDYRPI 281
                                               ********************************************************************* PP

                                 TIGR01196 278 aelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhf 346
                                               +e++de++ivna v llatGGstnh +hl aiar+aG++++wdd++ ls +vpllarvypnG+advn f
  lcl|FitnessBrowser__Korea:Ga0059261_0354 282 GEIVDERAIVNAAVVLLATGGSTNHLIHLPAIARCAGVLIDWDDFDRLSRVVPLLARVYPNGSADVNGF 350
                                               ********************************************************************* PP

                                 TIGR01196 347 eaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsa 415
                                               e aGG +f+irel+k G+lh d+ tvag  l  y + p+led+ l++++   ks d++ilr++d pfs+
  lcl|FitnessBrowser__Korea:Ga0059261_0354 351 EDAGGPTFVIRELIKGGVLHGDTLTVAGDSLADYVRRPVLEDDTLVWKDHGAKSGDDSILRTIDAPFSE 419
                                               ********************************************************************* PP

                                 TIGR01196 416 eGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmp 484
                                               eGG ++l+GnlGra ikvsav+ +   ieap++vf +q+e+++afkagel+rd+v+vvrfqGp+anGmp
  lcl|FitnessBrowser__Korea:Ga0059261_0354 420 EGGFRILSGNLGRACIKVSAVERDRWTIEAPCRVFATQQEVQDAFKAGELDRDVVVVVRFQGPRANGMP 488
                                               ********************************************************************* PP

                                 TIGR01196 485 elhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngele 553
                                               elhklt++lGvlq++gf+valvtdGr+sGasGkvpaaih++pea+ gG++ k+rdGd++rl a +g l+
  lcl|FitnessBrowser__Korea:Ga0059261_0354 489 ELHKLTPPLGVLQNKGFRVALVTDGRMSGASGKVPAAIHLSPEAIGGGPIGKLRDGDVVRLCAEEGILQ 557
                                               ********************************************************************* PP

                                 TIGR01196 554 vlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                                lv+ ae++arel+      ++lG+Grelfa++r  +s ae G+s++
  lcl|FitnessBrowser__Korea:Ga0059261_0354 558 ALVEPAEWEARELAAA--PPPDLGTGRELFAMMRAGASEAEAGGSAM 602
                                               ************7654..5688*********************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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.15
//
[ok]

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

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Protein sequences (fasta format)
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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