Alignments for a candidate for icd in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Caulobacter crescentus NA1000

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate CCNA_02607 CCNA_02607 isocitrate dehydrogenase

Query= BRENDA::B7GQR3
         (406 letters)



>FitnessBrowser__Caulo:CCNA_02607
          Length = 403

 Score =  602 bits (1552), Expect = e-177
 Identities = 290/405 (71%), Positives = 337/405 (83%), Gaps = 2/405 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           MAKIKV   VV++DGDEMTR+IWK IKD+LI PYLD+ LDYYDL +E+RD TDDQVTIDA
Sbjct: 1   MAKIKVANPVVDMDGDEMTRIIWKLIKDKLIFPYLDLELDYYDLSVENRDATDDQVTIDA 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           A+A +KH V VKCATITPDE RV+EF LKKMWKSPNGTIRNILGG IFREPI+  NVPRL
Sbjct: 61  ANATKKHGVAVKCATITPDEQRVEEFKLKKMWKSPNGTIRNILGGVIFREPIICQNVPRL 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWT+PI+V RHAFGDQY+ATDFK PG G L++ F  +DG + I+H V+    D GVA 
Sbjct: 121 VPGWTQPIIVGRHAFGDQYRATDFKFPGKGTLSIKFVGEDG-QTIEHEVFK-APDAGVAM 178

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN+++SIR FA A F YGL R YPVYLSTKNTILKAYDG+FKDIF E+++ EY +K+ 
Sbjct: 179 AMYNLDESIRDFAHASFAYGLNRGYPVYLSTKNTILKAYDGRFKDIFQEIYDAEYAEKFK 238

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
            AG+ YEHRLIDDMVAS+LKW GGY+WACKNYDGDVQSD VAQGFGSLGLMTSVLMTPDG
Sbjct: 239 AAGIHYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDG 298

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           +TVE+EAAHGTVTRHYR+ QKGE TSTN IASIFAWT GL HRA LD   ++ +FA TLE
Sbjct: 299 KTVEAEAAHGTVTRHYRQHQKGESTSTNSIASIFAWTRGLAHRAKLDDNQDLANFAATLE 358

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405
           KV +DTVE G MTKDLA+L+G  + WL T+GF++ +DENL KA+A
Sbjct: 359 KVCIDTVESGYMTKDLALLVGDKQGWLTTEGFLDKIDENLKKAMA 403


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: 671
Number of extensions: 26
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: 406
Length of database: 403
Length adjustment: 31
Effective length of query: 375
Effective length of database: 372
Effective search space:   139500
Effective search space used:   139500
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 CCNA_02607 CCNA_02607 (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.9821.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-220  717.0   0.8   2.8e-220  716.9   0.8    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02607  CCNA_02607 isocitrate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02607  CCNA_02607 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.9   0.8  2.8e-220  2.8e-220       2     407 ..       3     402 ..       2     403 .] 0.99

  Alignments for each domain:
  == domain 1  score: 716.9 bits;  conditional E-value: 2.8e-220
                             TIGR00127   2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkcat 74 
                                           kikvanpvv++dgdemtriiw+likdkli+pyl+l+l yydlsve+rdat+d+vt daa+a+kk++vavkcat
  lcl|FitnessBrowser__Caulo:CCNA_02607   3 KIKVANPVVDMDGDEMTRIIWKLIKDKLIFPYLDLELDYYDLSVENRDATDDQVTIDAANATKKHGVAVKCAT 75 
                                           9************************************************************************ PP

                             TIGR00127  75 itpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvpg 147
                                           itpde+rv+efklkkmwkspngtirnilgg +frepii++++prlvp+w++pii+grhafgdqy+atd+  pg
  lcl|FitnessBrowser__Caulo:CCNA_02607  76 ITPDEQRVEEFKLKKMWKSPNGTIRNILGGVIFREPIICQNVPRLVPGWTQPIIVGRHAFGDQYRATDFKFPG 148
                                           ************************************************************************* PP

                             TIGR00127 148 pgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkydg 220
                                           +g l + ++ +d +++++ +v++ ++ g va+amyn desi+dfa+as++  l++++p+ylstkntilk ydg
  lcl|FitnessBrowser__Caulo:CCNA_02607 149 KGTLSIKFVGED-GQTIEHEVFKAPDAG-VAMAMYNLDESIRDFAHASFAYGLNRGYPVYLSTKNTILKAYDG 219
                                           *********987.5899******99987.******************************************** PP

                             TIGR00127 221 rfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmtsv 293
                                           rfkdifqe+y+++y +kf+a+gi+yehrliddmva alk  ggy++a+knydgdvqsdivaqgfgslglmtsv
  lcl|FitnessBrowser__Caulo:CCNA_02607 220 RFKDIFQEIYDAEYAEKFKAAGIHYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSV 292
                                           ************************************************************************* PP

                             TIGR00127 294 lvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatietv 366
                                           l+tpdgktveaeaahgtvtrhyr++qkge tstnsiasifaw+rgl++rakld++ +l++fa +le+++i+tv
  lcl|FitnessBrowser__Caulo:CCNA_02607 293 LMTPDGKTVEAEAAHGTVTRHYRQHQKGESTSTNSIASIFAWTRGLAHRAKLDDNQDLANFAATLEKVCIDTV 365
                                           ************************************************************************* PP

                             TIGR00127 367 eegimtkdlalilkksklersayltteefldaveerlkkkl 407
                                           e+g mtkdlal+++++    + +ltte fld+++e+lkk +
  lcl|FitnessBrowser__Caulo:CCNA_02607 366 ESGYMTKDLALLVGDK----QGWLTTEGFLDKIDENLKKAM 402
                                           *************988....89****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (403 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: 9.27
//
[ok]

This GapMind analysis is from Sep 17 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