Alignments for a candidate for icd in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Rhodobacter ovatus JA234

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_097029409.1 CRO07_RS04135 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::B7GQR3
         (406 letters)



>NCBI__GCF_900207575.1:WP_097029409.1
          Length = 404

 Score =  587 bits (1513), Expect = e-172
 Identities = 283/404 (70%), Positives = 337/404 (83%), Gaps = 2/404 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           M+KIKV   VVELDGDEMTR+IW  IK +LILPYLD++L YYDLGIE RD T DQ+TIDA
Sbjct: 1   MSKIKVANPVVELDGDEMTRIIWDFIKQKLILPYLDIDLHYYDLGIEERDRTQDQITIDA 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           AHAI+K+ VGVKCATITPDEARV+EFGLK+MWKSPNGTIRNILGG IFR+PI+  NVPRL
Sbjct: 61  AHAIKKYGVGVKCATITPDEARVEEFGLKQMWKSPNGTIRNILGGVIFRQPIICKNVPRL 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWT+PIVV RHAFGDQY+ATDF+ PG G+LT+ F  +DG+  I+  V++     GV  
Sbjct: 121 VPGWTQPIVVGRHAFGDQYRATDFRFPGKGKLTLKFVGEDGTV-IERDVFD-APGAGVTM 178

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN+++SI  FARA  NYGL   +PVYLSTKNTILKAYDG+FKD+F +V+E E+++K+ 
Sbjct: 179 AMYNLDESILDFARASMNYGLNLGWPVYLSTKNTILKAYDGRFKDLFQKVYEEEFEEKFK 238

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
             G+ YEHRLIDDMVAS+LKW GGY+WACKNYDGDVQSD+VAQGFGSLGLMTSVLMTPDG
Sbjct: 239 AKGIHYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSVLMTPDG 298

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           QTVE+EAAHGTVTRHYR+ Q G++TSTN IASIFAWTGGLKHRA LD   ++  FA+TLE
Sbjct: 299 QTVEAEAAHGTVTRHYRQHQAGKETSTNSIASIFAWTGGLKHRAKLDNNADLMRFAETLE 358

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKAL 404
           +V V TVE G MTKDLA+L+GP++ WL T G++  +DE L +AL
Sbjct: 359 RVTVQTVEDGHMTKDLALLVGPNQKWLTTMGYLEKVDEYLDRAL 402


Lambda     K      H
   0.318    0.136    0.416 

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: 669
Number of extensions: 22
Number of successful extensions: 2
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: 406
Length of database: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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_097029409.1 CRO07_RS04135 (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.287399.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-212  691.6   0.1   1.5e-212  691.5   0.1    1.0  1  NCBI__GCF_900207575.1:WP_097029409.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900207575.1:WP_097029409.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.5   0.1  1.5e-212  1.5e-212       1     406 [.       2     401 ..       2     404 .] 0.98

  Alignments for each domain:
  == domain 1  score: 691.5 bits;  conditional E-value: 1.5e-212
                             TIGR00127   1 kkikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkca 73 
                                           +kikvanpvveldgdemtriiw+ ik+klilpyl++dl+yydl++e+rd+t+d++t daa+aikky+v+vkca
  NCBI__GCF_900207575.1:WP_097029409.1   2 SKIKVANPVVELDGDEMTRIIWDFIKQKLILPYLDIDLHYYDLGIEERDRTQDQITIDAAHAIKKYGVGVKCA 74 
                                           59*********************************************************************** PP

                             TIGR00127  74 titpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvp 146
                                           titpdearv+ef lk+mwkspngtirnilgg +fr+pii+k++prlvp+w++pi++grhafgdqy+atd+  p
  NCBI__GCF_900207575.1:WP_097029409.1  75 TITPDEARVEEFGLKQMWKSPNGTIRNILGGVIFRQPIICKNVPRLVPGWTQPIVVGRHAFGDQYRATDFRFP 147
                                           ************************************************************************* PP

                             TIGR00127 147 gpgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkyd 219
                                           g+gkl l ++ +dg+  ++  v+d ++ g v++amyn desi dfa+as++  l+ ++p+ylstkntilk yd
  NCBI__GCF_900207575.1:WP_097029409.1 148 GKGKLTLKFVGEDGT-VIERDVFDAPGAG-VTMAMYNLDESILDFARASMNYGLNLGWPVYLSTKNTILKAYD 218
                                           ***********9987.57889****9998.******************************************* PP

                             TIGR00127 220 grfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmts 292
                                           grfkd+fq+vye+++ +kf+a+gi+yehrliddmva alk  ggy++a+knydgdvqsd+vaqgfgslglmts
  NCBI__GCF_900207575.1:WP_097029409.1 219 GRFKDLFQKVYEEEFEEKFKAKGIHYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDTVAQGFGSLGLMTS 291
                                           ************************************************************************* PP

                             TIGR00127 293 vlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatiet 365
                                           vl+tpdg+tveaeaahgtvtrhyr++q g+etstnsiasifaw+ gl +rakldn+a+l++fae+le +t++t
  NCBI__GCF_900207575.1:WP_097029409.1 292 VLMTPDGQTVEAEAAHGTVTRHYRQHQAGKETSTNSIASIFAWTGGLKHRAKLDNNADLMRFAETLERVTVQT 364
                                           ************************************************************************* PP

                             TIGR00127 366 veegimtkdlalilkksklersayltteefldaveerlkkk 406
                                           ve+g mtkdlal+++ +    +++ltt  +l++v+e l + 
  NCBI__GCF_900207575.1:WP_097029409.1 365 VEDGHMTKDLALLVGPN----QKWLTTMGYLEKVDEYLDRA 401
                                           ***************99....89***********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (404 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.65
//
[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