Alignments for a candidate for gnd in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Azospirillum brasilense Sp245

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate AZOBR_RS15725 AZOBR_RS15725 6-phosphogluconate dehydrogenase

Query= BRENDA::P80859
         (469 letters)



>FitnessBrowser__azobra:AZOBR_RS15725
          Length = 460

 Score =  450 bits (1157), Expect = e-131
 Identities = 228/463 (49%), Positives = 312/463 (67%), Gaps = 7/463 (1%)

Query: 6   IGVIGLAVMGKNLALNIESRGFSVSVYNRSSSKTEEFLQEAKGKNVVGTYSIEEFVQSLE 65
           I V+GL VMG+NLA N+   G  V+ Y+    +   F   A+  N V   S+EE + +L+
Sbjct: 1   IAVLGLGVMGRNLAANLADHGAVVAGYDLDEGRRGAFA--AQVANAVPCASVEELLGALK 58

Query: 66  TPRKILLMVKAGTATDATIQSLLPHLEKDDILIDGGNTYYKDTQRRNKELAESGIHFIGT 125
            PR IL+MV AG   D    +LLP L   D+LIDGGN++++DT RR    A +G+ F+G 
Sbjct: 59  APRTILMMVPAGAPVDELTAALLPRLSPGDVLIDGGNSHFRDTNRRAALAAAAGVRFVGL 118

Query: 126 GVSGGEEGALKGPSIMPGGQKEAHELVKPILEAISAKV-DGEPCTTYIGPDGAGHYVKMV 184
           GVSGGEEGA +GP++M GG  EA   V P+L AI+A+  DGE C   +GP+GAGH+VKM+
Sbjct: 119 GVSGGEEGARRGPALMAGGDAEALAPVAPLLAAIAARAPDGESCFARVGPEGAGHFVKMI 178

Query: 185 HNGIEYGDMQLISESYFILKQVLGLSADELHEVFAEWNKGELDSYLIEITADIFTKKDEE 244
           HNGIEY DMQLI+E+Y +L+++ G S + L ++FA+WN GEL SYL+EIT DI   KD E
Sbjct: 179 HNGIEYADMQLIAEAYHLLREIGGCSYERLADIFADWNSGELASYLMEITTDILRTKDGE 238

Query: 245 TGKPLVDVILDKAGQKGTGKWTSQSALDLGVPLPIITESVFARFISAMKEERVKASGLLS 304
           +G P+++VI D AGQKGTG W + +AL+LG+P P I E+V AR +SA+K+ERV+A+  L+
Sbjct: 239 SGAPILEVIRDAAGQKGTGHWAATTALELGMPAPTIAEAVHARCLSALKDERVRAAEALA 298

Query: 305 GPEVKPVTENKEELIEAVRKALFMSKICSYAQGFAQMKAASEEYNWDLKYGEIAMIFRGG 364
            P       + E+L+ +V  AL   +I  YAQGFA + A S ++ WD+    +A I+RGG
Sbjct: 299 IPH----APSTEDLVASVGDALLSGRIAVYAQGFAVIAAGSRQFGWDVDLAAVARIWRGG 354

Query: 365 CIIRAAFLQKIKEAYDREPELDNLLLDSYFKNIVESYQGALRQVISLAVAQGVPVPSFSS 424
           CIIRA  L +I  A +R PEL NL+LD     ++       R+V++ A    VPVP+ +S
Sbjct: 355 CIIRARLLDRILTALNRAPELPNLMLDPDIAGLMTRGDAGFRRVVAAATLAAVPVPAMAS 414

Query: 425 ALAYYDSYRTAVLPANLIQAQRDYFGAHTYERTDKEGIFHTEW 467
           AL+Y+D YR+  L AN+IQAQRDYFGAH YERTD+ G+ HTEW
Sbjct: 415 ALSYWDGYRSGRLWANMIQAQRDYFGAHGYERTDRPGMVHTEW 457


Lambda     K      H
   0.315    0.134    0.379 

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: 497
Number of extensions: 13
Number of successful extensions: 4
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: 469
Length of database: 460
Length adjustment: 33
Effective length of query: 436
Effective length of database: 427
Effective search space:   186172
Effective search space used:   186172
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 (21.5 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS15725 AZOBR_RS15725 (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.17085.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-176  572.4   0.0   4.3e-176  572.2   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS15725  AZOBR_RS15725 6-phosphogluconate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS15725  AZOBR_RS15725 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.2   0.0  4.3e-176  4.3e-176       2     466 ..       1     458 [.       1     459 [. 0.98

  Alignments for each domain:
  == domain 1  score: 572.2 bits;  conditional E-value: 4.3e-176
                                 TIGR00873   2 iGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilll 70 
                                               i ++Gl+vmG+nl+ n+ad+G  va y+ ++ +  ++ ++     + v+  s+ee++ +l+ Pr il++
  lcl|FitnessBrowser__azobra:AZOBR_RS15725   1 IAVLGLGVMGRNLAANLADHGAVVAGYDLDEGRRGAFAAQ---VANAVPCASVEELLGALKAPRTILMM 66 
                                               6799*********************************998...55678999****************** PP

                                 TIGR00873  71 vkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmp 139
                                               v aGa+vd++ ++llp l +gd++idGGns+++dt+rr    +++g++fvG+GvsGGeeGar+GP+lm 
  lcl|FitnessBrowser__azobra:AZOBR_RS15725  67 VPAGAPVDELTAALLPRLSPGDVLIDGGNSHFRDTNRRAALAAAAGVRFVGLGVSGGEEGARRGPALMA 135
                                               ********************************************************************* PP

                                 TIGR00873 140 GGskeayelvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealkls 207
                                               GG++ea   v+p+l +iaa++  ge+c   +G++GaGh+vkm+hnGiey+dmqliaeay+ll+e+ + s
  lcl|FitnessBrowser__azobra:AZOBR_RS15725 136 GGDAEALAPVAPLLAAIAARAPdGESCFARVGPEGAGHFVKMIHNGIEYADMQLIAEAYHLLREIGGCS 204
                                               ********************977********************************************** PP

                                 TIGR00873 208 aeeiaevfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtl 275
                                               +e++a++f++Wn+gel syl+eit+dil++kd + G p++++i daagqkGtG+W+a+ al+lG+P  +
  lcl|FitnessBrowser__azobra:AZOBR_RS15725 205 YERLADIFADWNSGELASYLMEITTDILRTKDGEsGAPILEVIRDAAGQKGTGHWAATTALELGMPAPT 273
                                               ********************************988********************************** PP

                                 TIGR00873 276 itesvfarvlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskey 344
                                               i+e+v ar+ls+lk+erv+a++ l+ p+a ++    e+++ +v +al+ ++i  yaqGfa+++++s+++
  lcl|FitnessBrowser__azobra:AZOBR_RS15725 274 IAEAVHARCLSALKDERVRAAEALAIPHAPST----EDLVASVGDALLSGRIAVYAQGFAVIAAGSRQF 338
                                               **************************998877....59******************************* PP

                                 TIGR00873 345 gwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgi 413
                                               gwd++l+++a+iwrgGciir+++ld+i +a +  pel nl+l++  ++ +++   g+r+vva a+ +++
  lcl|FitnessBrowser__azobra:AZOBR_RS15725 339 GWDVDLAAVARIWRGGCIIRARLLDRILTALNRAPELPNLMLDPDIAGLMTRGDAGFRRVVAAATLAAV 407
                                               ********************************************************************* PP

                                 TIGR00873 414 pvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWl 466
                                               pvPa+++als++dgyr+ rl an++qaqrdyfGah+yertd+p+  ++hteW+
  lcl|FitnessBrowser__azobra:AZOBR_RS15725 408 PVPAMASALSYWDGYRSGRLWANMIQAQRDYFGAHGYERTDRPG--MVHTEWK 458
                                               ********************************************..9*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (460 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: 12.15
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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