Alignments for a candidate for gnd in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Escherichia coli BW25113

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate 16137 b2029 6-phosphogluconate dehydrogenase (NCBI)

Query= BRENDA::P00350
         (468 letters)



>FitnessBrowser__Keio:16137
          Length = 468

 Score =  925 bits (2391), Expect = 0.0
 Identities = 468/468 (100%), Positives = 468/468 (100%)

Query: 1   MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEF 60
           MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEF
Sbjct: 1   MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEF 60

Query: 61  VESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF 120
           VESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF
Sbjct: 61  VESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF 120

Query: 121 NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGH 180
           NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGH
Sbjct: 121 NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGH 180

Query: 181 YVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFT 240
           YVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFT
Sbjct: 181 YVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFT 240

Query: 241 KKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAAS 300
           KKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAAS
Sbjct: 241 KKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAAS 300

Query: 301 KVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIF 360
           KVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIF
Sbjct: 301 KVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIF 360

Query: 361 RAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT 420
           RAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT
Sbjct: 361 RAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT 420

Query: 421 FSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD 468
           FSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD
Sbjct: 421 FSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD 468


Lambda     K      H
   0.317    0.135    0.385 

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: 894
Number of extensions: 23
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: 468
Length of database: 468
Length adjustment: 33
Effective length of query: 435
Effective length of database: 435
Effective search space:   189225
Effective search space used:   189225
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate 16137 b2029 (6-phosphogluconate dehydrogenase (NCBI))
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.7954.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.1e-236  771.1   0.1   2.4e-236  770.9   0.1    1.0  1  lcl|FitnessBrowser__Keio:16137  b2029 6-phosphogluconate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16137  b2029 6-phosphogluconate dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  770.9   0.1  2.4e-236  2.4e-236       1     466 [.       5     467 ..       5     468 .] 0.99

  Alignments for each domain:
  == domain 1  score: 770.9 bits;  conditional E-value: 2.4e-236
                       TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilllvkaGaavda 79 
                                     +iG++G+avmG+nl+lni+++G++v+++nr++ekt+e+++e + gkklv++++++efv+sle+Pr+ill+vkaGa +da
  lcl|FitnessBrowser__Keio:16137   5 QIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAE-NPGKKLVPYYTVKEFVESLETPRRILLMVKAGAGTDA 82 
                                     69**************************************9.99*********************************** PP

                       TIGR00873  80 vieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayelvepilqkiaa 158
                                     +i++l+p+l+kgdiiidGGn++++dt+rr++el+++g++f+G+GvsGGeeGa+kGPs+mpGG+keayelv+pil+kiaa
  lcl|FitnessBrowser__Keio:16137  83 AIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAA 161
                                     ******************************************************************************* PP

                       TIGR00873 159 kve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWnegeldsylieitadilk 236
                                      +e gepc++yiG+dGaGhyvkmvhnGieygdmqliaeay+llk +l+l++ee+a++f+eWn+gel+syli+it+di++
  lcl|FitnessBrowser__Keio:16137 162 VAEdGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFT 240
                                     *999*************************************************************************** PP

                       TIGR00873 237 kkdedGkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaaskllsgplaeekaedkeefi 315
                                     kkdedG++lvd+ild+a++kGtGkWt+++aldlG P++litesvfar++sslk++rvaask+lsgp+a+ ++ dk+efi
  lcl|FitnessBrowser__Keio:16137 241 KKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASKVLSGPQAQPAG-DKAEFI 318
                                     *******************************************************************99998.****** PP

                       TIGR00873 316 edvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdal 394
                                     e+vr+aly++kivsyaqGf++l++as+ey+wdln+geia+i+r+Gciir++fl+ki++a++enp+++nllla+yfk++ 
  lcl|FitnessBrowser__Keio:16137 319 EKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIA 397
                                     ******************************************************************************* PP

                       TIGR00873 395 kkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWl 466
                                     +++q++lr+vva a+++gipvP++saa+++yd+yr+a+lpanl+qaqrdyfGahty+r+dk++  +fhteWl
  lcl|FitnessBrowser__Keio:16137 398 DDYQQALRDVVAYAVQNGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEG--VFHTEWL 467
                                     **************************************************************9..******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (468 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.67
//
[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