Alignments for a candidate for gnd in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Bacteroides thetaiotaomicron VPI-5482

Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (characterized)
to candidate 350750 BT1222 6-phosphogluconate dehydrogenase,decarboxylating (NCBI ptt file)

Query= CharProtDB::CH_122771
         (517 letters)



>FitnessBrowser__Btheta:350750
          Length = 491

 Score =  517 bits (1331), Expect = e-151
 Identities = 263/493 (53%), Positives = 347/493 (70%), Gaps = 16/493 (3%)

Query: 30  DIGLIGLAVMGQNLILNMADHGYTVVAYNRTT-----AKVDRFLENEAKGKSILGAHSIK 84
           DIGLIGLAVMG+NL LNM   G+ V  YNRT        VDRF+   AKGK+I G   IK
Sbjct: 8   DIGLIGLAVMGENLALNMESKGWHVSVYNRTVPGVEEGVVDRFMNGRAKGKNIEGFTDIK 67

Query: 85  ELVDQLKRPRRIMLLVKAGAPVDEFINQLLPYLEEGDIIIDGGNSHFPDSNRRYEELAKK 144
             V+ +  PR+IM++V+AG+PVDE ++QL P L  GDI+IDGGNS++ D+NRR +    K
Sbjct: 68  AFVESIATPRKIMMMVRAGSPVDELMDQLFPLLSPGDILIDGGNSNYEDTNRRVKLAESK 127

Query: 145 GILFVGSGVSGGEEGARTGPSLMPGGNEKAWPHIKDIFQDVAAKS-DGEPCCDWVGDAGA 203
           G LFVGSGVSGGEEGA  G S+MPGG+EKAWP +K + Q +AAK+ DG PCC WVG AG+
Sbjct: 128 GFLFVGSGVSGGEEGALNGASIMPGGSEKAWPEVKPVLQSIAAKAPDGTPCCQWVGPAGS 187

Query: 204 GHYVKMVHNGIEYGDMQLICEAYDLMKRVGKFEDKEIGDVFATWNKGVLDSFLIEITRDI 263
           GH+VKM+HNGIEYGDMQLI EAY +MK +    ++E+ DVFA WN+G L S+LIEIT +I
Sbjct: 188 GHFVKMIHNGIEYGDMQLIAEAYWVMKNLIDLTNEEMADVFARWNEGKLRSYLIEITSNI 247

Query: 264 LYYNDPTDGKPLVEKILDTAGQKGTGKWTAVNALDLGIPVTLIGEAVFSRCLSAMKAERV 323
           L + D + G  L++KILD AGQKGTGKW+ +NA++LG+P+ LI  AVF R LSA K  R 
Sbjct: 248 LRHKDKSGGY-LIDKILDAAGQKGTGKWSVINAMELGMPLGLIATAVFERSLSAQKELRH 306

Query: 324 EASKALKGPQVTGESPITDKKQFIDDLEQALYASKIISYTQGFMLMNQAAKDYGWKLNNA 383
            ASK           PI +K + + ++  ALYASK++SY QGF ++ +A+  +GW L+ A
Sbjct: 307 LASKQFLCKHTL---PIYNKAELVKEIFSALYASKLVSYAQGFAVLQRASDSFGWNLDLA 363

Query: 384 GIALMWRGGCIIRSVFLAEITAAYRKKPDLENLLLYPFFNDAITKAQSGWRASVGKAIQY 443
            IA MWRGGCIIRS+FL +I AA+      ++LLL P+F + I     GW+  V +A++ 
Sbjct: 364 SIARMWRGGCIIRSIFLNDIAAAFEAADKPKHLLLAPYFREEIKSLLPGWKNLVAEAMKE 423

Query: 444 GIPTPAFSTALAFYDGLRSERLPANLLQAQRDYFGAHTFKVLPGQENELLKKDEWIHINW 503
            +P PAFS+AL ++  L S+ LPANL+QAQRDYFGAHTF+    +++EL  + ++ H NW
Sbjct: 424 ELPVPAFSSALNYFYSLTSDNLPANLVQAQRDYFGAHTFE----RKDEL--RGQFFHENW 477

Query: 504 TGRGGDVSSTTYD 516
           TG GG+  S TY+
Sbjct: 478 TGHGGETKSGTYN 490


Lambda     K      H
   0.318    0.137    0.409 

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: 699
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: 517
Length of database: 491
Length adjustment: 34
Effective length of query: 483
Effective length of database: 457
Effective search space:   220731
Effective search space used:   220731
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: 52 (24.6 bits)

Align candidate 350750 BT1222 (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.3305.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.6e-210  683.9   0.0   6.4e-210  683.7   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350750  BT1222 6-phosphogluconate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350750  BT1222 6-phosphogluconate dehydrogenase,decarboxylating (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.7   0.0  6.4e-210  6.4e-210       1     466 [.       8     478 ..       8     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 683.7 bits;  conditional E-value: 6.4e-210
                          TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrt.....kektdellkeeakgkklvgaesieefvkslekPrkilllv 71 
                                        diGliGlavmG+nl+ln+++kG++v+vynrt     + ++d++++ +akgk+++g+++i+ fv+s+ +Prki+++v
  lcl|FitnessBrowser__Btheta:350750   8 DIGLIGLAVMGENLALNMESKGWHVSVYNRTvpgveEGVVDRFMNGRAKGKNIEGFTDIKAFVESIATPRKIMMMV 83 
                                        79****************************933332357899********************************** PP

                          TIGR00873  72 kaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeaye 147
                                        +aG++vd+++++l pll +gdi+idGGns+y+dt+rr+k  + kg+lfvG+GvsGGeeGa++G s+mpGGs++a++
  lcl|FitnessBrowser__Btheta:350750  84 RAGSPVDELMDQLFPLLSPGDILIDGGNSNYEDTNRRVKLAESKGFLFVGSGVSGGEEGALNGASIMPGGSEKAWP 159
                                        **************************************************************************** PP

                          TIGR00873 148 lvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWnege 222
                                        +v+p+lq+iaak+  g+pcc+++G++G+Gh+vkm+hnGieygdmqliaeay+++k+ ++l++ee+a+vf++Wneg+
  lcl|FitnessBrowser__Btheta:350750 160 EVKPVLQSIAAKAPdGTPCCQWVGPAGSGHFVKMIHNGIEYGDMQLIAEAYWVMKNLIDLTNEEMADVFARWNEGK 235
                                        ************977************************************************************* PP

                          TIGR00873 223 ldsylieitadilkkkdedGkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaaskl 298
                                        l sylieit++il++kd++G +l+dkildaagqkGtGkW++i+a++lG+P+ li+ +vf r ls++ke r  ask+
  lcl|FitnessBrowser__Btheta:350750 236 LRSYLIEITSNILRHKDKSGGYLIDKILDAAGQKGTGKWSVINAMELGMPLGLIATAVFERSLSAQKELRHLASKQ 311
                                        **************************************************************************** PP

                          TIGR00873 299 lsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkikka 374
                                        +  +++     +k+e+++++ +alyask+vsyaqGfa+l++as+++gw+l+l++ia++wrgGciirs fl+ i +a
  lcl|FitnessBrowser__Btheta:350750 312 FLCKHTLPIY-NKAELVKEIFSALYASKLVSYAQGFAVLQRASDSFGWNLDLASIARMWRGGCIIRSIFLNDIAAA 386
                                        *999888775.9**************************************************************** PP

                          TIGR00873 375 feenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGahty 450
                                        fe+  + ++llla+yf++++k+   g+++ va+a++  +pvPa+s+al+++ ++++++lpanl+qaqrdyfGaht+
  lcl|FitnessBrowser__Btheta:350750 387 FEAADKPKHLLLAPYFREEIKSLLPGWKNLVAEAMKEELPVPAFSSALNYFYSLTSDNLPANLVQAQRDYFGAHTF 462
                                        **************************************************************************** PP

                          TIGR00873 451 ertdkprgeffhteWl 466
                                        er+d+ rg+ffh +W+
  lcl|FitnessBrowser__Btheta:350750 463 ERKDELRGQFFHENWT 478
                                        ***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (491 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.53
//
[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