Alignments for a candidate for icd in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Rhizobium etli CFN 42

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_020921416.1 RHE_RS11845 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::B7GQR3
         (406 letters)



>NCBI__GCF_000092045.1:WP_020921416.1
          Length = 403

 Score =  610 bits (1574), Expect = e-179
 Identities = 294/405 (72%), Positives = 346/405 (85%), Gaps = 2/405 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           M KIKV   V +LDGDEMTR+IW+ IKD+LI PYLD+++DYYDL +E+RD T+DQVT+DA
Sbjct: 1   MKKIKVANPVADLDGDEMTRIIWQLIKDKLIHPYLDLDIDYYDLSVENRDATNDQVTVDA 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           A+AI+K+ VG+KCATITPDEARVKEF LK+MWKSPNGTIRNILGG IFREPI+  NVPRL
Sbjct: 61  ANAIKKYGVGIKCATITPDEARVKEFNLKEMWKSPNGTIRNILGGVIFREPIICRNVPRL 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWT+PIVV RHAFGDQY+ATDFK PG G+LT+ F  +DG+  I+  V+N     GVA 
Sbjct: 121 VPGWTQPIVVGRHAFGDQYRATDFKFPGKGKLTIKFVGEDGTV-IEKEVFN-APGAGVAM 178

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN+++SIR FARA   YGLMR +PVYLSTKNTILKAYDG+FKDIF EV+ETE+KD++ 
Sbjct: 179 AMYNLDESIREFARASMMYGLMRKWPVYLSTKNTILKAYDGRFKDIFEEVYETEFKDQFK 238

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
           EAG+TYEHRLIDDMVAS+LKW GGY+WACKNYDGDVQSD+VAQGFGSLGLMTSVL+TPDG
Sbjct: 239 EAGITYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSVLLTPDG 298

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           +TVE+EAAHGTVTRHYR+ QKG++TSTN IASIFAWT GL HRA LD   E+  FA TLE
Sbjct: 299 KTVEAEAAHGTVTRHYRQHQKGQETSTNSIASIFAWTRGLAHRAKLDDNAELAKFASTLE 358

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405
           KV VDTVE G MTKDLA+LIGPD+PWL T  F++ +D+NL KA+A
Sbjct: 359 KVCVDTVESGFMTKDLALLIGPDQPWLSTTAFLDKIDQNLQKAMA 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: 670
Number of extensions: 24
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: 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 WP_020921416.1 RHE_RS11845 (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.2043158.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-219  712.1   0.3   8.9e-219  711.9   0.3    1.0  1  NCBI__GCF_000092045.1:WP_020921416.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_020921416.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  711.9   0.3  8.9e-219  8.9e-219       1     407 [.       2     402 ..       2     403 .] 0.99

  Alignments for each domain:
  == domain 1  score: 711.9 bits;  conditional E-value: 8.9e-219
                             TIGR00127   1 kkikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkca 73 
                                           kkikvanpv +ldgdemtriiw+likdkli pyl+ld+ yydlsve+rdatnd+vt+daa+aikky+v++kca
  NCBI__GCF_000092045.1:WP_020921416.1   2 KKIKVANPVADLDGDEMTRIIWQLIKDKLIHPYLDLDIDYYDLSVENRDATNDQVTVDAANAIKKYGVGIKCA 74 
                                           69*********************************************************************** PP

                             TIGR00127  74 titpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvp 146
                                           titpdearvkef+lk+mwkspngtirnilgg +frepii++++prlvp+w++pi++grhafgdqy+atd+  p
  NCBI__GCF_000092045.1:WP_020921416.1  75 TITPDEARVKEFNLKEMWKSPNGTIRNILGGVIFREPIICRNVPRLVPGWTQPIVVGRHAFGDQYRATDFKFP 147
                                           ************************************************************************* PP

                             TIGR00127 147 gpgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkyd 219
                                           g+gkl + ++ +dg+  ++ +v++ ++ g va+amyn desi++fa+as+   l +k+p+ylstkntilk yd
  NCBI__GCF_000092045.1:WP_020921416.1 148 GKGKLTIKFVGEDGT-VIEKEVFNAPGAG-VAMAMYNLDESIREFARASMMYGLMRKWPVYLSTKNTILKAYD 218
                                           ***********9987.57889****9998.******************************************* PP

                             TIGR00127 220 grfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmts 292
                                           grfkdif+evye+++k++f+++gi yehrliddmva alk  ggy++a+knydgdvqsd+vaqgfgslglmts
  NCBI__GCF_000092045.1:WP_020921416.1 219 GRFKDIFEEVYETEFKDQFKEAGITYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDTVAQGFGSLGLMTS 291
                                           ************************************************************************* PP

                             TIGR00127 293 vlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatiet 365
                                           vl+tpdgktveaeaahgtvtrhyr++qkg+etstnsiasifaw+rgl++rakld++ael+kfa +le+++++t
  NCBI__GCF_000092045.1:WP_020921416.1 292 VLLTPDGKTVEAEAAHGTVTRHYRQHQKGQETSTNSIASIFAWTRGLAHRAKLDDNAELAKFASTLEKVCVDT 364
                                           ************************************************************************* PP

                             TIGR00127 366 veegimtkdlalilkksklersayltteefldaveerlkkkl 407
                                           ve+g+mtkdlal+++      + +l+t  fld+++++l+k +
  NCBI__GCF_000092045.1:WP_020921416.1 365 VESGFMTKDLALLIGPD----QPWLSTTAFLDKIDQNLQKAM 402
                                           ***************99....89***************9976 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.36
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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