Alignments for a candidate for gnd in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Echinicola vietnamensis KMM 6221, DSM 17526

Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (characterized)
to candidate Echvi_0478 Echvi_0478 6-phosphogluconate dehydrogenase, decarboxylating

Query= SwissProt::P70718
         (484 letters)



>FitnessBrowser__Cola:Echvi_0478
          Length = 636

 Score =  350 bits (897), Expect = e-100
 Identities = 179/468 (38%), Positives = 279/468 (59%), Gaps = 11/468 (2%)

Query: 8   GVIGLAVMGQNLILNMNDHGFKVVAYNRTTSKVDE-----FLEGAAKGTNIIGAYSLEDL 62
           G+IG+ VMG +L LN+ +   K+  YNRT   V+E      ++   +   I+    L++ 
Sbjct: 168 GIIGMGVMGSSLALNLAEKDVKISVYNRTLQGVEEDVAQKLVDAHPEVKGILPFDKLDEF 227

Query: 63  ANKLEKPRKVMLMVRAGEVVDHFIDALLPHLEAGDIIIDGGNSNYPDTNRRVAALREKGI 122
              LE+PRK+++M+ AG++VD  I  LL  ++ GD+IIDGGNS + D+ +R   L+  GI
Sbjct: 228 VESLEQPRKILMMIPAGQIVDQQIARLLTFVDKGDVIIDGGNSFFEDSAKRQQYLQGYGI 287

Query: 123 RFIGTGVSGGEEGARHGPSIMPGGNEEAWQFVKPVLQAISAKTEQGEPCCDWVGKDGAGH 182
            F+G G+SGG +GA  GPS+MPGG+EE ++ +KP L+ I+ K + G+PC  +VG DGAGH
Sbjct: 288 HFVGMGISGGRDGALKGPSLMPGGSEEGFELIKPYLEKIAGKDKGGKPCMHYVGPDGAGH 347

Query: 183 FVKMVHNGIEYGDMQLICEAYQFLKEGVGLSDDELQATFNEWRNTELDSYLIDITADILG 242
           F+KMVHN IEYG++Q++ E Y F+++G+G+S +E+  TF  W     DSYL+D T  IL 
Sbjct: 348 FIKMVHNSIEYGEIQVLAELYGFMRKGLGMSIEEMVKTFKTWSKEGADSYLMDATLAILS 407

Query: 243 YKDADGSRLVDKVLDTAGQKGTGKWTGINALDFGIPLTLITESVFARCVSAFKDQRVAAS 302
           + + DG  L+D +LD AGQ GTG W    A  +G+P   +T +V AR VS  K+ RV+ +
Sbjct: 408 H-EKDGKLLLDGILDVAGQTGTGGWAVSTAAKYGVPYAPLTAAVTARLVSTHKEARVSFA 466

Query: 303 KLFHKTIGKVEGDKKVWIEAVRKALLASKIISYAQGFMLIREASEHFNWNINYGNTALLW 362
           + + +   ++  D+K  I+A++ A   ++++++  GF LI++  E   W +N    A  W
Sbjct: 467 QTYPRKTDEI--DQKEIIDALKGAYDMARLVNHEIGFSLIKKVGEAEKWGLNMSEIARCW 524

Query: 363 REGCIIRSRFLGNIRDAYEANPDLIFLGSDSYFKGILENAMSDWRKVVAKSIEVGIPMPC 422
             G II+S  +  +   +++   L+   + +  K   EN      +VV   ++ GI MP 
Sbjct: 525 TNGSIIQSSLMEKLAGVFKSTDCLM---ASAALKASFENGAKTLAEVVGAGLKAGIAMPV 581

Query: 423 MASAITFLDGYTSARLPANLLQAQRDYFGAHTYERTDKPRGEFFHTNW 470
           M++AI F  G +S +  ANL+QA RD FG H Y   D   G+     W
Sbjct: 582 MSAAINFFYGMSSGQSSANLVQALRDCFGEHGYRLVDDVSGKIHRNKW 629


Lambda     K      H
   0.319    0.137    0.415 

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: 796
Number of extensions: 40
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 484
Length of database: 636
Length adjustment: 36
Effective length of query: 448
Effective length of database: 600
Effective search space:   268800
Effective search space used:   268800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate Echvi_0478 Echvi_0478 (6-phosphogluconate dehydrogenase, decarboxylating)
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))

# 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/TIGR00873.hmm
# target sequence database:        /tmp/gapView.16445.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00873  [M=467]
Accession:   TIGR00873
Description: gnd: 6-phosphogluconate dehydrogenase (decarboxylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.8e-146  472.9   0.6   7.1e-146  472.6   0.6    1.1  1  lcl|FitnessBrowser__Cola:Echvi_0478  Echvi_0478 6-phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0478  Echvi_0478 6-phosphogluconate dehydrogenase, decarboxylating
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.6   0.6  7.1e-146  7.1e-146       2     466 ..     167     630 ..     166     631 .. 0.95

  Alignments for each domain:
  == domain 1  score: 472.6 bits;  conditional E-value: 7.1e-146
                            TIGR00873   2 iGliGlavmGknlvlniadkGfsvavynrtkektd.....ellkeeakgkklvgaesieefvkslekPrkilll 70 
                                          +G+iG++vmG+ l+ln+a+k  +++vynrt + ++     +l+  + + k + ++ +++efv+sle+Prkil++
  lcl|FitnessBrowser__Cola:Echvi_0478 167 FGIIGMGVMGSSLALNLAEKDVKISVYNRTLQGVEedvaqKLVDAHPEVKGILPFDKLDEFVESLEQPRKILMM 240
                                          8****************************9776651111157777888999*********************** PP

                            TIGR00873  71 vkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGske 144
                                          + aG+ vd+ i++ll +++kgd+iidGGns+++d+ +r++ l+  gi+fvG+G+sGG +Ga+kGPslmpGGs+e
  lcl|FitnessBrowser__Cola:Echvi_0478 241 IPAGQIVDQQIARLLTFVDKGDVIIDGGNSFFEDSAKRQQYLQGYGIHFVGMGISGGRDGALKGPSLMPGGSEE 314
                                          ************************************************************************** PP

                            TIGR00873 145 ayelvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfee 217
                                           +el++p l+kia k + g+pc++y+G+dGaGh++kmvhn ieyg++q++ae y +++++l++s ee+ ++f++
  lcl|FitnessBrowser__Cola:Echvi_0478 315 GFELIKPYLEKIAGKDKgGKPCMHYVGPDGAGHFIKMVHNSIEYGEIQVLAELYGFMRKGLGMSIEEMVKTFKT 388
                                          ***************9999******************************************************* PP

                            TIGR00873 218 WnegeldsylieitadilkkkdedGkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkee 291
                                          W ++  dsyl++ t +il++ ++dGk l+d ild+agq GtG W++  a + GvP + +t++v ar++s+ ke+
  lcl|FitnessBrowser__Cola:Echvi_0478 389 WSKEGADSYLMDATLAILSH-EKDGKLLLDGILDVAGQTGTGGWAVSTAAKYGVPYAPLTAAVTARLVSTHKEA 461
                                          ******************86.689************************************************** PP

                            TIGR00873 292 rvaaskllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirs 365
                                          rv  +++++ ++    + d++e i++++ a  ++++v +  Gf+l+k++ +   w ln++eia+ w +G ii+s
  lcl|FitnessBrowser__Cola:Echvi_0478 462 RVSFAQTYPRKTD---EIDQKEIIDALKGAYDMARLVNHEIGFSLIKKVGEAEKWGLNMSEIARCWTNGSIIQS 532
                                          ***9999987654...35889***************************************************** PP

                            TIGR00873 366 kfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllq 439
                                          ++++k+   f++      l+ +  +k + ++  k+l +vv  + ++gi++P +saa++f+ g+++ +++anl+q
  lcl|FitnessBrowser__Cola:Echvi_0478 533 SLMEKLAGVFKST---DCLMASAALKASFENGAKTLAEVVGAGLKAGIAMPVMSAAINFFYGMSSGQSSANLVQ 603
                                          **********975...578889999999********************************************** PP

                            TIGR00873 440 aqrdyfGahtyertdkprgeffhteWl 466
                                          a+rd fG h+y+  d   g+ +  +W 
  lcl|FitnessBrowser__Cola:Echvi_0478 604 ALRDCFGEHGYRLVDDVSGKIHRNKWR 630
                                          ****************99999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (636 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: 9.67
//
[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