Alignments for a candidate for icd in Rhizobium subbaraonis JC85

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Rhizobium subbaraonis JC85

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_097140959.1 CRO48_RS16495 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::B7GQR3
         (406 letters)



>NCBI__GCF_900220975.1:WP_097140959.1
          Length = 404

 Score =  614 bits (1584), Expect = e-180
 Identities = 300/405 (74%), Positives = 343/405 (84%), Gaps = 2/405 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           MAKIKV   VVELDGDEMTR+IW+ IK++LI PYLD++L YYDL +E+RD TDDQVTIDA
Sbjct: 1   MAKIKVANPVVELDGDEMTRIIWQFIKEKLIHPYLDIDLKYYDLSVENRDATDDQVTIDA 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           A+AI+++ VGVKCATITPDE RV+EFGLKKMWKSPNGTIRNILGG IFREPI+  NVPRL
Sbjct: 61  ANAIKQYGVGVKCATITPDEGRVEEFGLKKMWKSPNGTIRNILGGVIFREPIICKNVPRL 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWTKPI+V RHAFGDQY+ATDFK PG G+LT+ F  +DG E I++ V++     GVA 
Sbjct: 121 VPGWTKPIIVGRHAFGDQYRATDFKFPGKGKLTMKFVGEDGKE-IEYDVFD-APSAGVAM 178

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN++DSI  FARA FNYGL R  PVYLSTKNTILK YDG+FKDIF EVF+ E+ +K+ 
Sbjct: 179 GMYNLDDSITEFARASFNYGLQRKVPVYLSTKNTILKVYDGRFKDIFQEVFDAEFAEKFK 238

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
           EA + YEHRLIDDMVAS+LKW GGY+WACKNYDGDVQSD VAQGFGSLGLMTSVLMTPDG
Sbjct: 239 EAKIWYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDG 298

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           QTVE+EAAHGTVTRHYR+ QKGE+TSTN IASIFAWT GL HRA LDG  E+  FA TLE
Sbjct: 299 QTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNTELAKFATTLE 358

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405
           KV VDTVE G MTKDLA+LIGPD+PWL T GF++ +DENL KA+A
Sbjct: 359 KVCVDTVESGFMTKDLALLIGPDQPWLSTTGFLDKIDENLQKAMA 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: 678
Number of extensions: 28
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: 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_097140959.1 CRO48_RS16495 (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.2132618.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-219  713.8   0.2   2.8e-219  713.6   0.2    1.0  1  NCBI__GCF_900220975.1:WP_097140959.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900220975.1:WP_097140959.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.6   0.2  2.8e-219  2.8e-219       2     408 ..       3     403 ..       2     404 .] 0.99

  Alignments for each domain:
  == domain 1  score: 713.6 bits;  conditional E-value: 2.8e-219
                             TIGR00127   2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkcat 74 
                                           kikvanpvveldgdemtriiw+ ik+kli pyl++dlkyydlsve+rdat+d+vt daa+aik+y+v+vkcat
  NCBI__GCF_900220975.1:WP_097140959.1   3 KIKVANPVVELDGDEMTRIIWQFIKEKLIHPYLDIDLKYYDLSVENRDATDDQVTIDAANAIKQYGVGVKCAT 75 
                                           9************************************************************************ PP

                             TIGR00127  75 itpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvpg 147
                                           itpde rv+ef lkkmwkspngtirnilgg +frepii+k++prlvp+w+kpii+grhafgdqy+atd+  pg
  NCBI__GCF_900220975.1:WP_097140959.1  76 ITPDEGRVEEFGLKKMWKSPNGTIRNILGGVIFREPIICKNVPRLVPGWTKPIIVGRHAFGDQYRATDFKFPG 148
                                           ************************************************************************* PP

                             TIGR00127 148 pgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkydg 220
                                           +gkl + ++ +dg +++++ v+d +  g va++myn d+si +fa+as++  l++k+p+ylstkntilk ydg
  NCBI__GCF_900220975.1:WP_097140959.1 149 KGKLTMKFVGEDG-KEIEYDVFDAPSAG-VAMGMYNLDDSITEFARASFNYGLQRKVPVYLSTKNTILKVYDG 219
                                           *********9986.679******99887.******************************************** PP

                             TIGR00127 221 rfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmtsv 293
                                           rfkdifqev+++++ +kf++++iwyehrliddmva alk  ggy++a+knydgdvqsdivaqgfgslglmtsv
  NCBI__GCF_900220975.1:WP_097140959.1 220 RFKDIFQEVFDAEFAEKFKEAKIWYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSV 292
                                           ************************************************************************* PP

                             TIGR00127 294 lvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatietv 366
                                           l+tpdg+tveaeaahgtvtrhyr++qkgeetstnsiasifaw+rgl++rakld ++el+kfa +le+++++tv
  NCBI__GCF_900220975.1:WP_097140959.1 293 LMTPDGQTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNTELAKFATTLEKVCVDTV 365
                                           ************************************************************************* PP

                             TIGR00127 367 eegimtkdlalilkksklersayltteefldaveerlkkkle 408
                                           e+g+mtkdlal+++      + +l+t  fld+++e+l+k ++
  NCBI__GCF_900220975.1:WP_097140959.1 366 ESGFMTKDLALLIGPD----QPWLSTTGFLDKIDENLQKAMA 403
                                           **************99....89****************9876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.80
//
[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