Alignments for a candidate for icd in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Erythrobacter marinus HWDM-33

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_047093429.1 AAV99_RS07675 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::A5U813
         (409 letters)



>NCBI__GCF_001013305.1:WP_047093429.1
          Length = 409

 Score =  578 bits (1491), Expect = e-170
 Identities = 284/403 (70%), Positives = 325/403 (80%), Gaps = 3/403 (0%)

Query: 6   KIKVSGPVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAY 65
           KI+V  PVVELDGDEMT++IW+ I++ LILPYLD+ L YYDL IE RD TDDQ+TIDAA 
Sbjct: 3   KIQVKNPVVELDGDEMTKIIWQWIRERLILPYLDVDLKYYDLSIEKRDETDDQITIDAAN 62

Query: 66  AIKKHGVGVKCATITPDEARVEEFNLKKMWLSPNGTIRNILGGTIFREPIVISNVPRLVP 125
           AIK+HGVGVKCATITPDEARVEEF LK+MW SPNGTIRNILGG +FREPIVI NVPRLVP
Sbjct: 63  AIKEHGVGVKCATITPDEARVEEFGLKQMWRSPNGTIRNILGGVVFREPIVIDNVPRLVP 122

Query: 126 GWTKPIVIGRHAFGDQYRATNFKVDQPGTVTLTFTPADGSAPIVHEMVSIPEDGGVVLGM 185
           GWT PIV+GRHAFGDQYRAT+  +   G + L F  ADG    +   V   E  GV + M
Sbjct: 123 GWTDPIVVGRHAFGDQYRATDTLIPGAGKLRLVFEGADGKN--IDLDVFEFEQPGVAMAM 180

Query: 186 YNFKESIRDFARASFSYGLNAKWPVYLSTKNTILKAYDGMFKDEFERVYEEE-FKAQFEA 244
           YN  ESIRDFARASF+YGL+  WPVYLSTKNTILK YDG FKD F+ +++ E FK +FE 
Sbjct: 181 YNLDESIRDFARASFNYGLDRGWPVYLSTKNTILKKYDGRFKDLFQEIFDTEGFKEKFEE 240

Query: 245 AGLTYEHRLIDDMVAACLKWEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTADGK 304
           A +TYEHRLIDDMVAA LKW G +VWACKNYDGDVQSD VAQG+GSLGLMTSVLMT DG 
Sbjct: 241 ANITYEHRLIDDMVAAALKWSGKFVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDGN 300

Query: 305 TVEAEAAHGTVTRHYRQYQAGKPTSTNPIASIFAWTRGLQHRGKLDGTPEVIDFAHKLES 364
           TVEAEAAHGTVTRH+RQ++ GK TSTNPIASIFAWTRGL +RG+ D TP+V+ FA  LE 
Sbjct: 301 TVEAEAAHGTVTRHFRQHEQGKATSTNPIASIFAWTRGLMYRGRFDNTPDVVAFAETLER 360

Query: 365 VVIATVESGKMTKDLAILIGPEQDWLNSEEFLDAIADNLEKEL 407
           V I  VE GKMTKDLA+LIGP Q W+ +E+F +AI + LE E+
Sbjct: 361 VCIECVEQGKMTKDLALLIGPSQSWMTTEQFFEAIVEGLEVEM 403


Lambda     K      H
   0.318    0.136    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: 634
Number of extensions: 19
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: 409
Length of database: 409
Length adjustment: 31
Effective length of query: 378
Effective length of database: 378
Effective search space:   142884
Effective search space used:   142884
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: 50 (23.9 bits)

Align candidate WP_047093429.1 AAV99_RS07675 (NADP-dependent isocitrate dehydrogenase)
to HMM TIGR00127 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

# 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/TIGR00127.hmm
# target sequence database:        /tmp/gapView.2813132.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00127  [M=409]
Accession:   TIGR00127
Description: nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.3e-214  695.4   0.0   1.1e-213  695.2   0.0    1.0  1  NCBI__GCF_001013305.1:WP_047093429.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001013305.1:WP_047093429.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.2   0.0  1.1e-213  1.1e-213       2     408 ..       3     404 ..       2     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 695.2 bits;  conditional E-value: 1.1e-213
                             TIGR00127   2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkcat 74 
                                           ki+v+npvveldgdemt+iiw+ i+++lilpyl++dlkyydls+e+rd+t+d++t daa+aik ++v+vkcat
  NCBI__GCF_001013305.1:WP_047093429.1   3 KIQVKNPVVELDGDEMTKIIWQWIRERLILPYLDVDLKYYDLSIEKRDETDDQITIDAANAIKEHGVGVKCAT 75 
                                           9************************************************************************ PP

                             TIGR00127  75 itpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvpg 147
                                           itpdearv+ef lk+mw+spngtirnilgg vfrepi+i+++prlvp+w+ pi++grhafgdqy+atd+++pg
  NCBI__GCF_001013305.1:WP_047093429.1  76 ITPDEARVEEFGLKQMWRSPNGTIRNILGGVVFREPIVIDNVPRLVPGWTDPIVVGRHAFGDQYRATDTLIPG 148
                                           ************************************************************************* PP

                             TIGR00127 148 pgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkydg 220
                                            gkl+lv++  dg +++dl v+++e+ g va+amyn desi+dfa+as++  l++++p+ylstkntilkkydg
  NCBI__GCF_001013305.1:WP_047093429.1 149 AGKLRLVFEGADG-KNIDLDVFEFEQPG-VAMAMYNLDESIRDFARASFNYGLDRGWPVYLSTKNTILKKYDG 219
                                           ********99875.789*******9887.******************************************** PP

                             TIGR00127 221 rfkdifqevyek.qykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmts 292
                                           rfkd+fqe++++ ++k+kfe+++i yehrliddmva alk  g +++a+knydgdvqsdivaqgfgslglmts
  NCBI__GCF_001013305.1:WP_047093429.1 220 RFKDLFQEIFDTeGFKEKFEEANITYEHRLIDDMVAAALKWSGKFVWACKNYDGDVQSDIVAQGFGSLGLMTS 292
                                           **********9637*********************************************************** PP

                             TIGR00127 293 vlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatiet 365
                                           vl+tpdg tveaeaahgtvtrh+r++++g+ tstn+iasifaw+rgl+ r+++dnt+++v fae+le ++ie 
  NCBI__GCF_001013305.1:WP_047093429.1 293 VLMTPDGNTVEAEAAHGTVTRHFRQHEQGKATSTNPIASIFAWTRGLMYRGRFDNTPDVVAFAETLERVCIEC 365
                                           ************************************************************************* PP

                             TIGR00127 366 veegimtkdlalilkksklersayltteefldaveerlkkkle 408
                                           ve+g+mtkdlal+++ s    ++++tte+f++a+ e l+ +++
  NCBI__GCF_001013305.1:WP_047093429.1 366 VEQGKMTKDLALLIGPS----QSWMTTEQFFEAIVEGLEVEMK 404
                                           ***************99....89************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (409 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: 13.70
//
[ok]

This GapMind analysis is from Sep 24 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