GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Nocardiopsis lucentensis DSM 44048

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_017597063.1 D471_RS0101915 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::A5U813
         (409 letters)



>NCBI__GCF_000341125.1:WP_017597063.1
          Length = 405

 Score =  654 bits (1688), Expect = 0.0
 Identities = 309/403 (76%), Positives = 353/403 (87%)

Query: 6   KIKVSGPVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAY 65
           KIKV  PVVELDGDEMTR+IW  IKD LILPYLDI L YYDLGIE RD TDDQVT+D+A 
Sbjct: 3   KIKVENPVVELDGDEMTRIIWSFIKDRLILPYLDIDLKYYDLGIEERDRTDDQVTVDSAN 62

Query: 66  AIKKHGVGVKCATITPDEARVEEFNLKKMWLSPNGTIRNILGGTIFREPIVISNVPRLVP 125
           AIK++GVGVKCATITPDEARVEEF LKKMW SPNGTIRNILGG +FREPI+  NVPRLVP
Sbjct: 63  AIKQYGVGVKCATITPDEARVEEFGLKKMWRSPNGTIRNILGGVVFREPIICENVPRLVP 122

Query: 126 GWTKPIVIGRHAFGDQYRATNFKVDQPGTVTLTFTPADGSAPIVHEMVSIPEDGGVVLGM 185
           GWTKP++IGRHA GDQY+AT+FKV  PG+VT+T+TPADG  P+  E+ + PE GGV +GM
Sbjct: 123 GWTKPVIIGRHAHGDQYKATDFKVPGPGSVTMTYTPADGGEPVEFEVANFPEGGGVAMGM 182

Query: 186 YNFKESIRDFARASFSYGLNAKWPVYLSTKNTILKAYDGMFKDEFERVYEEEFKAQFEAA 245
           YNF++SI DFARAS +YGL+  +PVY+STKNTILKAYDGMFKD F+ +YE EFK +F+AA
Sbjct: 183 YNFRKSIEDFARASLNYGLDRNYPVYMSTKNTILKAYDGMFKDVFQEIYETEFKEKFDAA 242

Query: 246 GLTYEHRLIDDMVAACLKWEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTADGKT 305
           GLTYEHRLIDDMVAA LKWEGGYVWACKNYDGDVQSDTVAQG+GSLGLMTSVL TADG+T
Sbjct: 243 GLTYEHRLIDDMVAAALKWEGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSVLRTADGRT 302

Query: 306 VEAEAAHGTVTRHYRQYQAGKPTSTNPIASIFAWTRGLQHRGKLDGTPEVIDFAHKLESV 365
           VEAEAAHGTVTRHYRQ+Q GKPTSTNPIASIFAWTRGL+HR KLD TP++ +FA+ LE V
Sbjct: 303 VEAEAAHGTVTRHYRQHQQGKPTSTNPIASIFAWTRGLEHRAKLDNTPKLTEFANTLEDV 362

Query: 366 VIATVESGKMTKDLAILIGPEQDWLNSEEFLDAIADNLEKELA 408
           VI TVE G+MTKDLA+L+G EQ+WL +E+FL A+ +NL K LA
Sbjct: 363 VIKTVEGGQMTKDLALLVGGEQEWLTTEQFLAALDENLSKRLA 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: 657
Number of extensions: 16
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_017597063.1 D471_RS0101915 (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.529475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-220  716.1   0.0   5.3e-220  716.0   0.0    1.0  1  NCBI__GCF_000341125.1:WP_017597063.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341125.1:WP_017597063.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.0   0.0  5.3e-220  5.3e-220       2     407 ..       3     404 ..       2     405 .] 0.99

  Alignments for each domain:
  == domain 1  score: 716.0 bits;  conditional E-value: 5.3e-220
                             TIGR00127   2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkcat 74 
                                           kikv+npvveldgdemtriiw+ ikd+lilpyl++dlkyydl++e+rd+t+d+vt+d+a+aik+y+v+vkcat
  NCBI__GCF_000341125.1:WP_017597063.1   3 KIKVENPVVELDGDEMTRIIWSFIKDRLILPYLDIDLKYYDLGIEERDRTDDQVTVDSANAIKQYGVGVKCAT 75 
                                           9************************************************************************ PP

                             TIGR00127  75 itpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvpg 147
                                           itpdearv+ef lkkmw+spngtirnilgg vfrepii++++prlvp+w+kp+iigrha+gdqykatd+ vpg
  NCBI__GCF_000341125.1:WP_017597063.1  76 ITPDEARVEEFGLKKMWRSPNGTIRNILGGVVFREPIICENVPRLVPGWTKPVIIGRHAHGDQYKATDFKVPG 148
                                           ************************************************************************* PP

                             TIGR00127 148 pgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkydg 220
                                           pg++ ++y+p dg+e+v+++v +++e ggva++myn  +siedfa+asl+  l++++p+y+stkntilk ydg
  NCBI__GCF_000341125.1:WP_017597063.1 149 PGSVTMTYTPADGGEPVEFEVANFPEGGGVAMGMYNFRKSIEDFARASLNYGLDRNYPVYMSTKNTILKAYDG 221
                                           ************************************************************************* PP

                             TIGR00127 221 rfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmtsv 293
                                            fkd+fqe+ye+++k+kf+a+g+ yehrliddmva alk +ggy++a+knydgdvqsd+vaqgfgslglmtsv
  NCBI__GCF_000341125.1:WP_017597063.1 222 MFKDVFQEIYETEFKEKFDAAGLTYEHRLIDDMVAAALKWEGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSV 294
                                           ************************************************************************* PP

                             TIGR00127 294 lvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatietv 366
                                           l t dg+tveaeaahgtvtrhyr++q+g+ tstn+iasifaw+rgl +rakldnt++l++fa++le+++i+tv
  NCBI__GCF_000341125.1:WP_017597063.1 295 LRTADGRTVEAEAAHGTVTRHYRQHQQGKPTSTNPIASIFAWTRGLEHRAKLDNTPKLTEFANTLEDVVIKTV 367
                                           ************************************************************************* PP

                             TIGR00127 367 eegimtkdlalilkksklersayltteefldaveerlkkkl 407
                                           e g mtkdlal+++++    +++ltte+fl a++e+l k+l
  NCBI__GCF_000341125.1:WP_017597063.1 368 EGGQMTKDLALLVGGE----QEWLTTEQFLAALDENLSKRL 404
                                           ***************9....89***************9987 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.96
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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