Alignments for a candidate for icd in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Azospirillum brasilense Sp245

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate AZOBR_RS10995 AZOBR_RS10995 isocitrate dehydrogenase

Query= BRENDA::B7GQR3
         (406 letters)



>FitnessBrowser__azobra:AZOBR_RS10995
          Length = 407

 Score =  602 bits (1551), Expect = e-177
 Identities = 288/405 (71%), Positives = 341/405 (84%), Gaps = 1/405 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           M KIKV   VVELDGDEMTR+IW+ IKD+LILPYLDV+L YYDL +E+RD+TDD+VT+++
Sbjct: 1   MTKIKVANPVVELDGDEMTRIIWQFIKDKLILPYLDVDLKYYDLSVENRDKTDDRVTVES 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           A+AI+++ VGVKCATITPDEARV EF LKKMWKSPNGTIRNILGGT+FREPIV SNVPR 
Sbjct: 61  ANAIKQYGVGVKCATITPDEARVTEFNLKKMWKSPNGTIRNILGGTVFREPIVCSNVPRY 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWTKPI++ RHAFGDQYKATDF VPG G+LT+ + P+ G EPI+  VY++   G VA 
Sbjct: 121 VPGWTKPIIIGRHAFGDQYKATDFVVPGKGKLTIKWVPEGGGEPIEQEVYDFPASG-VAM 179

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN+++SI GFA + F YGL R YPVYLSTKNTILKAYDG+FKDIF +VF+  Y  ++ 
Sbjct: 180 GMYNLDESIEGFAHSSFMYGLERGYPVYLSTKNTILKAYDGRFKDIFQKVFDEHYAAQFK 239

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
             GL YEHRLIDDMVAS+LKW GG++WACKNYDGDVQSD VAQGFGSLGLMTSVL+TPDG
Sbjct: 240 AKGLVYEHRLIDDMVASALKWEGGFVWACKNYDGDVQSDIVAQGFGSLGLMTSVLITPDG 299

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           +TVE+EAAHGTVTRHYR  QKG++TSTNPIASI+AWT GL +R   D TP+V  FA+TLE
Sbjct: 300 KTVEAEAAHGTVTRHYREHQKGKETSTNPIASIYAWTQGLAYRGKFDNTPDVVKFAETLE 359

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405
           +V V+TVE G MTKDLA+LIGPD+PWL T  F++ LDENL K +A
Sbjct: 360 RVCVETVESGFMTKDLAILIGPDQPWLTTKQFLDKLDENLQKKMA 404


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: 689
Number of extensions: 23
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: 407
Length adjustment: 31
Effective length of query: 375
Effective length of database: 376
Effective search space:   141000
Effective search space used:   141000
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 AZOBR_RS10995 AZOBR_RS10995 (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.2837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-224  729.7   0.1   4.1e-224  729.5   0.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS10995  AZOBR_RS10995 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS10995  AZOBR_RS10995 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.5   0.1  4.1e-224  4.1e-224       1     408 [.       2     404 ..       2     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 729.5 bits;  conditional E-value: 4.1e-224
                                 TIGR00127   1 kkikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynva 69 
                                               +kikvanpvveldgdemtriiw+ ikdklilpyl++dlkyydlsve+rd+t+d+vt+++a+aik+y+v+
  lcl|FitnessBrowser__azobra:AZOBR_RS10995   2 TKIKVANPVVELDGDEMTRIIWQFIKDKLILPYLDVDLKYYDLSVENRDKTDDRVTVESANAIKQYGVG 70 
                                               69******************************************************************* PP

                                 TIGR00127  70 vkcatitpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqy 138
                                               vkcatitpdearv ef+lkkmwkspngtirnilggtvfrepi++ ++pr vp+w+kpiiigrhafgdqy
  lcl|FitnessBrowser__azobra:AZOBR_RS10995  71 VKCATITPDEARVTEFNLKKMWKSPNGTIRNILGGTVFREPIVCSNVPRYVPGWTKPIIIGRHAFGDQY 139
                                               ********************************************************************* PP

                                 TIGR00127 139 katdvvvpgpgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklply 207
                                               katd+vvpg+gkl + ++p++g+e+++ +vyd++ +g va++myn desie+fa++s+   le+++p+y
  lcl|FitnessBrowser__azobra:AZOBR_RS10995 140 KATDFVVPGKGKLTIKWVPEGGGEPIEQEVYDFPASG-VAMGMYNLDESIEGFAHSSFMYGLERGYPVY 207
                                               **********************************998.******************************* PP

                                 TIGR00127 208 lstkntilkkydgrfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvq 276
                                               lstkntilk ydgrfkdifq+v++++y  +f+a+g+ yehrliddmva alk +gg+++a+knydgdvq
  lcl|FitnessBrowser__azobra:AZOBR_RS10995 208 LSTKNTILKAYDGRFKDIFQKVFDEHYAAQFKAKGLVYEHRLIDDMVASALKWEGGFVWACKNYDGDVQ 276
                                               ********************************************************************* PP

                                 TIGR00127 277 sdivaqgfgslglmtsvlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakl 345
                                               sdivaqgfgslglmtsvl+tpdgktveaeaahgtvtrhyr++qkg+etstn+iasi+aw++gl+ r+k+
  lcl|FitnessBrowser__azobra:AZOBR_RS10995 277 SDIVAQGFGSLGLMTSVLITPDGKTVEAEAAHGTVTRHYREHQKGKETSTNPIASIYAWTQGLAYRGKF 345
                                               ********************************************************************* PP

                                 TIGR00127 346 dntaelvkfaeilesatietveegimtkdlalilkksklersayltteefldaveerlkkkle 408
                                               dnt+++vkfae+le +++etve+g+mtkdla++++      + +ltt++fld+++e+l+kk++
  lcl|FitnessBrowser__azobra:AZOBR_RS10995 346 DNTPDVVKFAETLERVCVETVESGFMTKDLAILIGPD----QPWLTTKQFLDKLDENLQKKMA 404
                                               **********************************999....89*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (407 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: 00:00:00.02
# Mc/sec: 7.22
//
[ok]

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

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

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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