Alignments for a candidate for icd in Nocardiopsis gilva YIM 90087

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Nocardiopsis gilva YIM 90087

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_094932740.1 CDO52_RS24670 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::A5U813
         (409 letters)



>NCBI__GCF_002263495.1:WP_094932740.1
          Length = 405

 Score =  659 bits (1699), Expect = 0.0
 Identities = 313/403 (77%), Positives = 351/403 (87%)

Query: 6   KIKVSGPVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAY 65
           KIKV  PVVELDGDEMTR+IW  IKD LILPYLD+ L YYDLGIE RD TDDQ+T+DAA 
Sbjct: 3   KIKVENPVVELDGDEMTRIIWSFIKDRLILPYLDVDLKYYDLGIEERDRTDDQITVDAAN 62

Query: 66  AIKKHGVGVKCATITPDEARVEEFNLKKMWLSPNGTIRNILGGTIFREPIVISNVPRLVP 125
           AIK++G GVKCATITPDEARVEEF LKKMW SPNGTIRNILGG +FREPI+  NVPRLVP
Sbjct: 63  AIKQYGAGVKCATITPDEARVEEFGLKKMWRSPNGTIRNILGGVVFREPIICQNVPRLVP 122

Query: 126 GWTKPIVIGRHAFGDQYRATNFKVDQPGTVTLTFTPADGSAPIVHEMVSIPEDGGVVLGM 185
           GWT+PI+IGRHA GDQY+A++FKV  PGTVT+T+TP DG  PI  E+ S PE GGV +GM
Sbjct: 123 GWTQPIIIGRHAHGDQYKASDFKVPGPGTVTITYTPEDGGEPIEMEVASFPEGGGVAMGM 182

Query: 186 YNFKESIRDFARASFSYGLNAKWPVYLSTKNTILKAYDGMFKDEFERVYEEEFKAQFEAA 245
           YNF++SI DFARASF YGL+  +PVYLSTKNTILKAYDGMFKD F  +YE E+K +FEAA
Sbjct: 183 YNFRKSIEDFARASFGYGLDRGYPVYLSTKNTILKAYDGMFKDVFAEIYEAEYKEKFEAA 242

Query: 246 GLTYEHRLIDDMVAACLKWEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTADGKT 305
           G+TYEHRLIDDMVAA LKWEGGYVWACKNYDGDVQSDTVAQG+GSLGLMTSVL TADG T
Sbjct: 243 GITYEHRLIDDMVAAALKWEGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSVLRTADGST 302

Query: 306 VEAEAAHGTVTRHYRQYQAGKPTSTNPIASIFAWTRGLQHRGKLDGTPEVIDFAHKLESV 365
           VEAEAAHGTVTRHYRQ+QAGKPTSTNPIASIFAWTRGL HRGKLD TP+V +FAH LE V
Sbjct: 303 VEAEAAHGTVTRHYRQHQAGKPTSTNPIASIFAWTRGLDHRGKLDNTPKVNEFAHALEDV 362

Query: 366 VIATVESGKMTKDLAILIGPEQDWLNSEEFLDAIADNLEKELA 408
           V+ TVE G+MTKDLA+L+G EQDWL +E+FL A+ +NL+K LA
Sbjct: 363 VVNTVEGGQMTKDLALLVGGEQDWLTTEQFLAALDENLQKRLA 405


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: 667
Number of extensions: 22
Number of successful extensions: 1
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: 405
Length adjustment: 31
Effective length of query: 378
Effective length of database: 374
Effective search space:   141372
Effective search space used:   141372
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_094932740.1 CDO52_RS24670 (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.2125190.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-218  709.9   0.0   4.1e-218  709.8   0.0    1.0  1  NCBI__GCF_002263495.1:WP_094932740.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002263495.1:WP_094932740.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  709.8   0.0  4.1e-218  4.1e-218       2     407 ..       3     404 ..       2     405 .] 1.00

  Alignments for each domain:
  == domain 1  score: 709.8 bits;  conditional E-value: 4.1e-218
                             TIGR00127   2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkcat 74 
                                           kikv+npvveldgdemtriiw+ ikd+lilpyl++dlkyydl++e+rd+t+d++t+daa+aik+y+ +vkcat
  NCBI__GCF_002263495.1:WP_094932740.1   3 KIKVENPVVELDGDEMTRIIWSFIKDRLILPYLDVDLKYYDLGIEERDRTDDQITVDAANAIKQYGAGVKCAT 75 
                                           9************************************************************************ PP

                             TIGR00127  75 itpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvpg 147
                                           itpdearv+ef lkkmw+spngtirnilgg vfrepii++++prlvp+w++piiigrha+gdqyka+d+ vpg
  NCBI__GCF_002263495.1:WP_094932740.1  76 ITPDEARVEEFGLKKMWRSPNGTIRNILGGVVFREPIICQNVPRLVPGWTQPIIIGRHAHGDQYKASDFKVPG 148
                                           ************************************************************************* PP

                             TIGR00127 148 pgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkydg 220
                                           pg + ++y+p+dg+e+++++v  ++e ggva++myn  +siedfa+as+   l++++p+ylstkntilk ydg
  NCBI__GCF_002263495.1:WP_094932740.1 149 PGTVTITYTPEDGGEPIEMEVASFPEGGGVAMGMYNFRKSIEDFARASFGYGLDRGYPVYLSTKNTILKAYDG 221
                                           ************************************************************************* PP

                             TIGR00127 221 rfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmtsv 293
                                            fkd+f e+ye++yk+kfea+gi yehrliddmva alk +ggy++a+knydgdvqsd+vaqgfgslglmtsv
  NCBI__GCF_002263495.1:WP_094932740.1 222 MFKDVFAEIYEAEYKEKFEAAGITYEHRLIDDMVAAALKWEGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSV 294
                                           ************************************************************************* PP

                             TIGR00127 294 lvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatietv 366
                                           l t dg tveaeaahgtvtrhyr++q g+ tstn+iasifaw+rgl +r+kldnt+++ +fa++le+++++tv
  NCBI__GCF_002263495.1:WP_094932740.1 295 LRTADGSTVEAEAAHGTVTRHYRQHQAGKPTSTNPIASIFAWTRGLDHRGKLDNTPKVNEFAHALEDVVVNTV 367
                                           ************************************************************************* PP

                             TIGR00127 367 eegimtkdlalilkksklersayltteefldaveerlkkkl 407
                                           e g mtkdlal+++++    +++ltte+fl a++e+l+k+l
  NCBI__GCF_002263495.1:WP_094932740.1 368 EGGQMTKDLALLVGGE----QDWLTTEQFLAALDENLQKRL 404
                                           ***************9....9*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (405 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: 00:00:00.00
# Mc/sec: 24.45
//
[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