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.31435.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.52
//
[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:

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