Alignments for a candidate for gnd in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Dyella japonica UNC79MFTsu3.2

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate N515DRAFT_4155 N515DRAFT_4155 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44)

Query= BRENDA::Q762L5
         (468 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4155
          Length = 473

 Score =  692 bits (1786), Expect = 0.0
 Identities = 345/463 (74%), Positives = 400/463 (86%), Gaps = 2/463 (0%)

Query: 6   IGVVGMAVMGRNLALNIESRGYTVSVFNRSREKTEEVIAENPGKKLVPYYTVQEFVESLE 65
           IGVVGMAVMGRNLALNIESRG+TV+++NRSREKT+EV+AE+P K+L P YT+QEFV++L+
Sbjct: 10  IGVVGMAVMGRNLALNIESRGHTVAIYNRSREKTDEVVAEHPDKRLAPTYTLQEFVDALQ 69

Query: 66  TPRRILLMVKAGAGTDSAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGT 125
            PRRILLMVKAG  TD+ I  LKP LD+GD++IDGGNTFFQDTIRR REL+A G +FIGT
Sbjct: 70  KPRRILLMVKAGEATDATIAELKPLLDQGDVLIDGGNTFFQDTIRRERELNAAGLHFIGT 129

Query: 126 GVSGGEEGALKGPSIMPGGQKEAYELVAPILKQIAAVAEDGEPCVTYIGADGAGHYVKMV 185
           GVSGGEEGAL GPSIMPGG ++AY+LVAP+L +IAA A DGEPCV Y+G +GAGHYVKMV
Sbjct: 130 GVSGGEEGALHGPSIMPGGPRDAYDLVAPVLTEIAARAPDGEPCVAYMGPNGAGHYVKMV 189

Query: 186 HNGIEYGDMQLIAEAYALLKGGLALSNEELAQTFTEWNEGELSSYLIDITKDIFTKKD-E 244
           HNGIEYGDMQLIAE+YA+LK  L LSNEEL + + EWN+GEL SYLI IT DIF K+D +
Sbjct: 190 HNGIEYGDMQLIAESYAVLKQVLGLSNEELGKVYAEWNQGELDSYLIAITADIFGKQDPD 249

Query: 245 EGKYLVDVILDEAANKGTGKWTSQSSLDLGEPLSLITESVFARYISSLKDQRVAASKVLS 304
            GK +VD+ILD AA KGTGKWTSQS+LDL  PL LITESVFAR +S+LKD+RVAASKVL 
Sbjct: 250 TGKAMVDIILDRAAQKGTGKWTSQSALDLAVPLPLITESVFARLLSALKDERVAASKVLK 309

Query: 305 GPQAQP-AGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASDEYNWDLNYGEIAKIFRAG 363
           GPQAQP AGD+A FIE VRRALYL KIVSYAQGF+QLRAASDEY W+L YG IAKIFRAG
Sbjct: 310 GPQAQPFAGDRAAFIESVRRALYLSKIVSYAQGFAQLRAASDEYKWNLPYGTIAKIFRAG 369

Query: 364 CIIRAQFLQKITDAYAQNAGIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPTFSA 423
           CIIRA+FLQKITDAYA +A +ANLLL PYF+ IA  YQQALRDVV+ AVQ G+ VP F++
Sbjct: 370 CIIRARFLQKITDAYAHDAALANLLLDPYFRDIAAQYQQALRDVVSAAVQAGVAVPGFAS 429

Query: 424 AIAYYDSYRSAVLPANLIQAQRDYFGAHTYKRTDKEGIFHTEW 466
           AIAYYDSYR+  LPANL+QAQRDYFGAHT++R D+ G FH +W
Sbjct: 430 AIAYYDSYRAERLPANLVQAQRDYFGAHTFERIDRPGSFHADW 472


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: 727
Number of extensions: 26
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: 473
Length adjustment: 33
Effective length of query: 435
Effective length of database: 440
Effective search space:   191400
Effective search space used:   191400
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 N515DRAFT_4155 N515DRAFT_4155 (6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))
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.14494.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.5e-221  722.0   0.0   1.8e-221  721.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155  N515DRAFT_4155 6-phosphogluconat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4155  N515DRAFT_4155 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.8   0.0  1.8e-221  1.8e-221       2     466 ..      10     473 .]       9     473 .] 0.99

  Alignments for each domain:
  == domain 1  score: 721.8 bits;  conditional E-value: 1.8e-221
                                    TIGR00873   2 iGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrki 67 
                                                  iG++G+avmG+nl+lni+++G++va+ynr++ektde+++e + +k+l ++++++efv++l+kPr+i
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155  10 IGVVGMAVMGRNLALNIESRGHTVAIYNRSREKTDEVVAE-HPDKRLAPTYTLQEFVDALQKPRRI 74 
                                                  8***************************************.7899********************* PP

                                    TIGR00873  68 lllvkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGark 133
                                                  ll+vkaG+a+da+i+el+pll++gd++idGGn++++dt+rre+el+++g++f+G+GvsGGeeGa++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155  75 LLMVKAGEATDATIAELKPLLDQGDVLIDGGNTFFQDTIRRERELNAAGLHFIGTGVSGGEEGALH 140
                                                  ****************************************************************** PP

                                    TIGR00873 134 GPslmpGGskeayelvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeaye 198
                                                  GPs+mpGG ++ay+lv+p+l++iaa++  gepc+ y+G++GaGhyvkmvhnGieygdmqliae+y 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155 141 GPSIMPGGPRDAYDLVAPVLTEIAARAPdGEPCVAYMGPNGAGHYVKMVHNGIEYGDMQLIAESYA 206
                                                  **************************977************************************* PP

                                    TIGR00873 199 llkealklsaeeiaevfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWta 263
                                                  +lk++l+ls+ee+ +v++eWn+geldsyli itadi+ k+d d Gk++vd ild+a+qkGtGkWt+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155 207 VLKQVLGLSNEELGKVYAEWNQGELDSYLIAITADIFGKQDPDtGKAMVDIILDRAAQKGTGKWTS 272
                                                  ******************************************99********************** PP

                                    TIGR00873 264 idaldlGvPvtlitesvfarvlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivs 329
                                                  ++aldl vP+ litesvfar+ls+lk+ervaask+l+gp+a+  a d+++fie+vr+aly+skivs
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155 273 QSALDLAVPLPLITESVFARLLSALKDERVAASKVLKGPQAQPFAGDRAAFIESVRRALYLSKIVS 338
                                                  ****************************************************************** PP

                                    TIGR00873 330 yaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalk 395
                                                  yaqGfa+l++as+ey w+l +g+ia+i+r+Gciir++fl+ki++a++++  l+nlll++yf+d+  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155 339 YAQGFAQLRAASDEYKWNLPYGTIAKIFRAGCIIRARFLQKITDAYAHDAALANLLLDPYFRDIAA 404
                                                  ****************************************************************** PP

                                    TIGR00873 396 kaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeff 461
                                                  ++q++lr+vv+ a+++g++vP++++a+++yd+yr++rlpanl+qaqrdyfGaht+er+d+p+   f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155 405 QYQQALRDVVSAAVQAGVAVPGFASAIAYYDSYRAERLPANLVQAQRDYFGAHTFERIDRPG--SF 468
                                                  **************************************************************..9* PP

                                    TIGR00873 462 hteWl 466
                                                  h++W+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4155 469 HADWT 473
                                                  ****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (473 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.66
//
[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