Alignments for a candidate for gnd in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Shewanella oneidensis MR-1

Align phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (characterized)
to candidate 201063 SO1902 6-phosphogluconate dehydrogenase, decarboxylating (NCBI ptt file)

Query= CharProtDB::CH_125393
         (492 letters)



>FitnessBrowser__MR1:201063
          Length = 508

 Score =  428 bits (1100), Expect = e-124
 Identities = 240/499 (48%), Positives = 313/499 (62%), Gaps = 35/499 (7%)

Query: 8   DFGLIGLAVMGQNLILNGADKGFTVCCYNRTTSRVDEFLANEAKGK-----SIVGAHSLE 62
           D G+IGL VMG+NL LN AD  + V  ++    +V+  L  E + +      I G  +L 
Sbjct: 9   DIGVIGLGVMGKNLALNIADNQYRVSVFDLDPVKVNGVLQQEKQERVGQELRITGCANLS 68

Query: 63  EFVSKLKKPRVCILLVKAGKPVDYLIEGLAPL-LEKGDIIVDGGNSHYPDTTRRCEELAK 121
           E ++ L KPR+ +L V AG PVD +   L    +E  DI++D GNS + DT  R E+  +
Sbjct: 69  EMLASLTKPRILVLSVPAGAPVDGVCAALISAGIEADDIVIDTGNSLWTDTVER-EQHYQ 127

Query: 122 KGILFVGSGVSGGEEGARYGPSLMPGGNPAAWPRIKPIFQTLAAKA-------------G 168
              +F  S VSGGE GAR+GPSLMP G+  AW  + PI++ +AAK              G
Sbjct: 128 GQFIFFSSAVSGGEVGARFGPSLMPSGDLGAWQHVAPIWKAIAAKVNPQTGLPIERFEPG 187

Query: 169 N----NEPCCDWVGEQGAGHYVKMVHNGIEYGDMQLICETYDIMKRGLGMSCDEIADVFE 224
           N     EPC  ++G  GAGHYVKMVHNGIEY DMQLICE Y ++  GLGMS  E+ +VFE
Sbjct: 188 NPVTEGEPCTTYIGPAGAGHYVKMVHNGIEYADMQLICEAYQLLHDGLGMSAAEVGEVFE 247

Query: 225 KWNTGKLDSFLIEITRDVLRYKADD--GKPLVEKILDAAGQKGTGKWTAQNALEMGTPVS 282
           +WN G L+S+L+ I+ +VL+ +AD   GKPLVE ILD AGQKGTG WTA ++L++G P  
Sbjct: 248 RWNQGSLNSYLMGISAEVLK-QADPLTGKPLVEMILDKAGQKGTGLWTAVSSLQIGCPAP 306

Query: 283 LITEAVFARCLSSLKSERVRASKKLTGPNTKFTGD--KKQLIDDLEDALYASKIISYAQG 340
            I EAV+AR +S+ KS RV  SKKL GP +    +  K  LID LE ALY +K+  YAQG
Sbjct: 307 TIAEAVYARAVSTQKSLRVELSKKLAGPLSPAMDENQKANLIDALESALYCAKVCCYAQG 366

Query: 341 FMLMREAAKEYGWKLNNAGIALMWRGGCIIRSVFLKDITEAFREDPNLESILFHPFFTNG 400
           F LM   A E  W+L+ A IA +WR GCIIR+ FL+ IT+A++ D NL  +L    F + 
Sbjct: 367 FQLMAMTALEQKWQLDFAEIAKIWRAGCIIRATFLQSITQAYQADANLSCLLMADTFAST 426

Query: 401 VEKAQAGWRRVVAQAAMLGIPVPATSTGLSFYDGYRSAVLPANLLQAQRDYFGAHTFRVL 460
           + + Q  WR  VA A M GIPVP  S+ L++YD YRS  LPANLLQ QRD+FGAHTF   
Sbjct: 427 LSEKQTEWRIAVAAAIMQGIPVPCISSALAYYDSYRSETLPANLLQGQRDFFGAHTF--- 483

Query: 461 PEAADKSLPADKDIHINWT 479
            E  DK  PA +  H++W+
Sbjct: 484 -ERLDK--PAGEKYHLDWS 499


Lambda     K      H
   0.319    0.137    0.414 

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: 633
Number of extensions: 27
Number of successful extensions: 6
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: 492
Length of database: 508
Length adjustment: 34
Effective length of query: 458
Effective length of database: 474
Effective search space:   217092
Effective search space used:   217092
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: 52 (24.6 bits)

Align candidate 201063 SO1902 (6-phosphogluconate dehydrogenase, decarboxylating (NCBI ptt file))
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.24466.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.6e-180  586.8   0.1   3.7e-179  582.3   0.1    2.0  1  lcl|FitnessBrowser__MR1:201063  SO1902 6-phosphogluconate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201063  SO1902 6-phosphogluconate dehydrogenase, decarboxylating (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.3   0.1  3.7e-179  3.7e-179       1     466 [.       9     499 ..       9     500 .. 0.94

  Alignments for each domain:
  == domain 1  score: 582.3 bits;  conditional E-value: 3.7e-179
                       TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgk.....klvgaesieefvkslekPrkilllvkaG 74 
                                     diG+iGl+vmGknl+lniad+ + v+v++ ++ k++ +l++e++++     +++g  ++ e+++sl kPr ++l v aG
  lcl|FitnessBrowser__MR1:201063   9 DIGVIGLGVMGKNLALNIADNQYRVSVFDLDPVKVNGVLQQEKQERvgqelRITGCANLSEMLASLTKPRILVLSVPAG 87 
                                     79*************************************998765433333799************************* PP

                       TIGR00873  75 aavdavieellpl.lekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayelvepi 152
                                     a+vd v ++l+ + +e  di+id Gnsl++dt  re++ + +   f  + vsGGe Gar+GPslmp G+  a+++v+pi
  lcl|FitnessBrowser__MR1:201063  88 APVDGVCAALISAgIEADDIVIDTGNSLWTDTVEREQHYQGQF-IFFSSAVSGGEVGARFGPSLMPSGDLGAWQHVAPI 165
                                     *******99876549*********************9998765.577899***************************** PP

                       TIGR00873 153 lqkiaakv..................egepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiae 213
                                      ++iaakv                  egepc++yiG++GaGhyvkmvhnGiey+dmqli+eay+ll+++l++sa e+ e
  lcl|FitnessBrowser__MR1:201063 166 WKAIAAKVnpqtglpierfepgnpvtEGEPCTTYIGPAGAGHYVKMVHNGIEYADMQLICEAYQLLHDGLGMSAAEVGE 244
                                     ******974444444443333333324789************************************************* PP

                       TIGR00873 214 vfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkee 291
                                     vfe+Wn+g+l+syl+ i+a++lk+ d   Gkplv++ild+agqkGtG Wta+++l+ G P  +i+e+v+ar++s++k+ 
  lcl|FitnessBrowser__MR1:201063 245 VFERWNQGSLNSYLMGISAEVLKQADPLtGKPLVEMILDKAGQKGTGLWTAVSSLQIGCPAPTIAEAVYARAVSTQKSL 323
                                     **************************977************************************************** PP

                       TIGR00873 292 rvaaskllsgplaeekae.dkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfld 369
                                     rv+ sk+l+gpl+  + e +k+++i+++++aly++k+++yaqGf+l+++++ e  w+l+++eia+iwr+Gciir++fl+
  lcl|FitnessBrowser__MR1:201063 324 RVELSKKLAGPLSPAMDEnQKANLIDALESALYCAKVCCYAQGFQLMAMTALEQKWQLDFAEIAKIWRAGCIIRATFLQ 402
                                     **********9998876648999******************************************************** PP

                       TIGR00873 370 kikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGah 448
                                     +i++a++++ +l+ ll+a+ f+++l+++q+++r +va ai +gipvP++s+al++yd+yr+++lpanllq+qrd+fGah
  lcl|FitnessBrowser__MR1:201063 403 SITQAYQADANLSCLLMADTFASTLSEKQTEWRIAVAAAIMQGIPVPCISSALAYYDSYRSETLPANLLQGQRDFFGAH 481
                                     ******************************************************************************* PP

                       TIGR00873 449 tyertdkprgeffhteWl 466
                                     t+er dkp ge++h +W+
  lcl|FitnessBrowser__MR1:201063 482 TFERLDKPAGEKYHLDWS 499
                                     *****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (508 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 3.29
//
[ok]

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

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Steps (tab-delimited)
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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