Alignments for a candidate for gnd in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Burkholderia phytofirmans PsJN

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate BPHYT_RS29625 BPHYT_RS29625 6-phosphogluconate dehydrogenase

Query= BRENDA::Q762L5
         (468 letters)



>FitnessBrowser__BFirm:BPHYT_RS29625
          Length = 469

 Score =  689 bits (1779), Expect = 0.0
 Identities = 344/468 (73%), Positives = 400/468 (85%), Gaps = 2/468 (0%)

Query: 1   MSKQQIGVVGMAVMGRNLALNIESRGYTVSVFNRSREKTEEVIAENPGKKLVPYYTVQEF 60
           M KQ IGVVG+AVMGRNLALNIESRG+ VSV+NRSREKT+E+IAE P KKLVP +T++EF
Sbjct: 1   MGKQAIGVVGLAVMGRNLALNIESRGHAVSVYNRSREKTDELIAEYPDKKLVPAFTLEEF 60

Query: 61  VESLETPRRILLMVKAGAGTDSAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF 120
           VESLE PRRILLMVKAG GTD+ I+ LKP LDKGDI+IDGGNT F DTIRRN++L+  G 
Sbjct: 61  VESLEKPRRILLMVKAGEGTDATINQLKPLLDKGDILIDGGNTHFTDTIRRNQDLAKSGL 120

Query: 121 NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILKQIAAVAEDGEPCVTYIGADGAGH 180
           +FIGTGVSGGEEGALKGPSIMPGGQ++AY+LVAPIL +IAA A DGEPCV Y+G DGAGH
Sbjct: 121 HFIGTGVSGGEEGALKGPSIMPGGQRDAYDLVAPILTEIAAKAPDGEPCVAYMGPDGAGH 180

Query: 181 YVKMVHNGIEYGDMQLIAEAYALLKGGLALSNEELAQTFTEWNEGELSSYLIDITKDIFT 240
           +VKMVHNGIEYGDMQLIAE+YA+LK  + LSNEEL + +TEWN+GEL SYLI+IT  IF 
Sbjct: 181 FVKMVHNGIEYGDMQLIAESYAVLKQVVGLSNEELGKVYTEWNQGELDSYLIEITSKIFG 240

Query: 241 KKDEE-GKYLVDVILDEAANKGTGKWTSQSSLDLGEPLSLITESVFARYISSLKDQRVAA 299
           KKD+E GK LVDVILD AA KGTGKWTSQ++LDLG PL LITE+VFAR +SSLK QRVAA
Sbjct: 241 KKDDETGKDLVDVILDRAAQKGTGKWTSQNALDLGAPLPLITEAVFARVLSSLKTQRVAA 300

Query: 300 SKVLSGPQAQPAG-DKAEFIEKVRRALYLGKIVSYAQGFSQLRAASDEYNWDLNYGEIAK 358
           SKVL GP A+P G ++  FIE VRRALY  K++SYAQGF+QLRAAS+EY WDL+YG IAK
Sbjct: 301 SKVLEGPAAKPLGVERDAFIESVRRALYFSKVISYAQGFAQLRAASEEYKWDLDYGTIAK 360

Query: 359 IFRAGCIIRAQFLQKITDAYAQNAGIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPV 418
           IFRAGCIIRA+FLQKITDAY ++  IANLLL PYF+ IA +YQ ALR+VV  AV  G+PV
Sbjct: 361 IFRAGCIIRARFLQKITDAYTKDKAIANLLLDPYFRDIAKNYQAALREVVVAAVNAGVPV 420

Query: 419 PTFSAAIAYYDSYRSAVLPANLIQAQRDYFGAHTYKRTDKEGIFHTEW 466
           P F++AIAY+D+YRS  LPANL+QAQRD+FGAHT++R DK G FH  W
Sbjct: 421 PAFASAIAYFDAYRSERLPANLVQAQRDFFGAHTFERIDKPGSFHANW 468


Lambda     K      H
   0.316    0.135    0.382 

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: 752
Number of extensions: 22
Number of successful extensions: 3
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: 469
Length adjustment: 33
Effective length of query: 435
Effective length of database: 436
Effective search space:   189660
Effective search space used:   189660
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 BPHYT_RS29625 BPHYT_RS29625 (6-phosphogluconate dehydrogenase)
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.7255.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   8.3e-226  736.1   0.0   9.5e-226  735.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS29625  BPHYT_RS29625 6-phosphogluconate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS29625  BPHYT_RS29625 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  735.9   0.0  9.5e-226  9.5e-226       2     466 ..       6     469 .]       5     469 .] 0.99

  Alignments for each domain:
  == domain 1  score: 735.9 bits;  conditional E-value: 9.5e-226
                                TIGR00873   2 iGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilllv 71 
                                              iG++GlavmG+nl+lni+++G+ v+vynr++ektdel++e   +kklv+a ++eefv+slekPr+ill+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625   6 IGVVGLAVMGRNLALNIESRGHAVSVYNRSREKTDELIAE-YPDKKLVPAFTLEEFVESLEKPRRILLMV 74 
                                              9***************************************.78999************************ PP

                                TIGR00873  72 kaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGG 141
                                              kaG+ +da+i++l+pll+kgdi+idGGn++++dt+rr+++l++ g++f+G+GvsGGeeGa+kGPs+mpGG
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625  75 KAGEGTDATINQLKPLLDKGDILIDGGNTHFTDTIRRNQDLAKSGLHFIGTGVSGGEEGALKGPSIMPGG 144
                                              ********************************************************************** PP

                                TIGR00873 142 skeayelvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaee 210
                                              +++ay+lv+pil++iaak+  gepc+ y+G+dGaGh+vkmvhnGieygdmqliae+y +lk++++ls+ee
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625 145 QRDAYDLVAPILTEIAAKAPdGEPCVAYMGPDGAGHFVKMVHNGIEYGDMQLIAESYAVLKQVVGLSNEE 214
                                              ******************977************************************************* PP

                                TIGR00873 211 iaevfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlites 279
                                              + +v++eWn+geldsylieit++i+ kkd++ Gk lvd+ild+a+qkGtGkWt+++aldlG P+ lite+
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625 215 LGKVYTEWNQGELDSYLIEITSKIFGKKDDEtGKDLVDVILDRAAQKGTGKWTSQNALDLGAPLPLITEA 284
                                              *************************9998888************************************** PP

                                TIGR00873 280 vfarvlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdln 349
                                              vfarvlsslk +rvaask+l+gp a+  ++++++fie+vr+aly sk++syaqGfa+l++as+ey wdl+
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625 285 VFARVLSSLKTQRVAASKVLEGPAAKPLGVERDAFIESVRRALYFSKVISYAQGFAQLRAASEEYKWDLD 354
                                              ********************************************************************** PP

                                TIGR00873 350 lgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPals 419
                                              +g+ia+i+r+Gciir++fl+ki++a+++++ ++nlll++yf+d+ k++q +lr+vv+ a+++g+pvPa++
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625 355 YGTIAKIFRAGCIIRARFLQKITDAYTKDKAIANLLLDPYFRDIAKNYQAALREVVVAAVNAGVPVPAFA 424
                                              ********************************************************************** PP

                                TIGR00873 420 aalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWl 466
                                              +a++++d+yr++rlpanl+qaqrd+fGaht+er+dkp+   fh++W+
  lcl|FitnessBrowser__BFirm:BPHYT_RS29625 425 SAIAYFDAYRSERLPANLVQAQRDFFGAHTFERIDKPG--SFHANWS 469
                                              **************************************..9*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (469 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: 00:00:00.02
# Mc/sec: 8.57
//
[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