Alignments for a candidate for icd in Magnetovibrio blakemorei MV-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Magnetovibrio blakemorei MV-1

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_069958999.1 BEN30_RS14270 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::B7GQR3
         (406 letters)



>NCBI__GCF_001746755.1:WP_069958999.1
          Length = 406

 Score =  612 bits (1579), Expect = e-180
 Identities = 290/405 (71%), Positives = 344/405 (84%), Gaps = 1/405 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           M+KIKV   +VELDGDEMTR+IW  IK++LILPYLDV+L YYDL +E RDETDDQ+TIDA
Sbjct: 1   MSKIKVANPIVELDGDEMTRIIWDFIKNKLILPYLDVDLKYYDLSMEKRDETDDQITIDA 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           A AI+ + VGVKCATITPDE RVKEFGLK MWKSPNGTIRNILGGT+FR+PI+ SNVPRL
Sbjct: 61  AEAIKTYRVGVKCATITPDEDRVKEFGLKTMWKSPNGTIRNILGGTVFRKPIICSNVPRL 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWT+PIV+ RHAFGDQY+ATDF+VPGAG+LT+ F P+DG E I+  V+N+    GVA 
Sbjct: 121 VPGWTQPIVIGRHAFGDQYRATDFRVPGAGKLTMKFVPEDGGEVIEREVFNF-PSSGVAM 179

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN++DSI+GFAR+C NYGL   +PVYLSTKNTI+KAYDG+FKD+F EVF+TE+K K+ 
Sbjct: 180 SMYNLDDSIKGFARSCMNYGLDLGWPVYLSTKNTIMKAYDGRFKDLFQEVFDTEFKAKFD 239

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
            AG+TYEHRLIDDMVA ++KW GG++WACKNYDGDVQSD+VAQGFGSLGLMTSVL+TPDG
Sbjct: 240 AAGITYEHRLIDDMVACAMKWSGGFVWACKNYDGDVQSDTVAQGFGSLGLMTSVLLTPDG 299

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           QTVE+EAAHGTVTRHYR+ Q G++TSTNPIASIFAWT G+ +R   DGTP+V  FA+ LE
Sbjct: 300 QTVEAEAAHGTVTRHYRQHQAGKETSTNPIASIFAWTRGIAYRGKFDGTPDVVKFAEALE 359

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKALA 405
           KV V TVE G MTKDLA+LIGPD+ W+ T  F+  LDENL   +A
Sbjct: 360 KVCVATVEAGHMTKDLALLIGPDQAWMTTTQFLEKLDENLKAEMA 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: 681
Number of extensions: 19
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: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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_069958999.1 BEN30_RS14270 (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.2362901.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-217  706.5   0.0   4.5e-217  706.3   0.0    1.0  1  NCBI__GCF_001746755.1:WP_069958999.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001746755.1:WP_069958999.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  706.3   0.0  4.5e-217  4.5e-217       1     408 [.       2     404 ..       2     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 706.3 bits;  conditional E-value: 4.5e-217
                             TIGR00127   1 kkikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvavkca 73 
                                           +kikvanp+veldgdemtriiw+ ik+klilpyl++dlkyydls+e+rd+t+d++t daaeaik y v+vkca
  NCBI__GCF_001746755.1:WP_069958999.1   2 SKIKVANPIVELDGDEMTRIIWDFIKNKLILPYLDVDLKYYDLSMEKRDETDDQITIDAAEAIKTYRVGVKCA 74 
                                           59*********************************************************************** PP

                             TIGR00127  74 titpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqykatdvvvp 146
                                           titpde rvkef lk mwkspngtirnilggtvfr+pii+ ++prlvp+w++pi+igrhafgdqy+atd+ vp
  NCBI__GCF_001746755.1:WP_069958999.1  75 TITPDEDRVKEFGLKTMWKSPNGTIRNILGGTVFRKPIICSNVPRLVPGWTQPIVIGRHAFGDQYRATDFRVP 147
                                           ************************************************************************* PP

                             TIGR00127 147 gpgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplylstkntilkkyd 219
                                           g gkl + ++p+dg+e ++ +v++++ +g va++myn d+si++fa++ ++  l+ ++p+ylstknti+k yd
  NCBI__GCF_001746755.1:WP_069958999.1 148 GAGKLTMKFVPEDGGEVIEREVFNFPSSG-VAMSMYNLDDSIKGFARSCMNYGLDLGWPVYLSTKNTIMKAYD 219
                                           **************************998.******************************************* PP

                             TIGR00127 220 grfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqsdivaqgfgslglmts 292
                                           grfkd+fqev+++++k kf+a+gi yehrliddmva a+k  gg+++a+knydgdvqsd+vaqgfgslglmts
  NCBI__GCF_001746755.1:WP_069958999.1 220 GRFKDLFQEVFDTEFKAKFDAAGITYEHRLIDDMVACAMKWSGGFVWACKNYDGDVQSDTVAQGFGSLGLMTS 292
                                           ************************************************************************* PP

                             TIGR00127 293 vlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakldntaelvkfaeilesatiet 365
                                           vl+tpdg+tveaeaahgtvtrhyr++q g+etstn+iasifaw+rg++ r+k+d t+++vkfae+le++++ t
  NCBI__GCF_001746755.1:WP_069958999.1 293 VLLTPDGQTVEAEAAHGTVTRHYRQHQAGKETSTNPIASIFAWTRGIAYRGKFDGTPDVVKFAEALEKVCVAT 365
                                           ************************************************************************* PP

                             TIGR00127 366 veegimtkdlalilkksklersayltteefldaveerlkkkle 408
                                           ve+g mtkdlal+++      +a++tt +fl++++e+lk++++
  NCBI__GCF_001746755.1:WP_069958999.1 366 VEAGHMTKDLALLIGPD----QAWMTTTQFLEKLDENLKAEMA 404
                                           ***************99....89*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (406 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: 26.94
//
[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