Alignments for a candidate for ilvC in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Sinorhizobium meliloti 1021

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate SMc04346 SMc04346 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>FitnessBrowser__Smeli:SMc04346
          Length = 339

 Score =  462 bits (1189), Expect = e-135
 Identities = 227/339 (66%), Positives = 272/339 (80%), Gaps = 1/339 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59
           M+V+YD+DADL+LIK K V IIGYGSQG AHALNLKDSG  NV + L+   A+  KA   
Sbjct: 1   MRVYYDRDADLNLIKSKKVAIIGYGSQGRAHALNLKDSGAQNVAIALKSGSATAKKAEAD 60

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           G +V  VAEA   AD++M+  PDE  AD+YK ++  NI++GAA+AFAHG NVH+G + P+
Sbjct: 61  GFKVMTVAEAAAWADLMMMATPDELQADIYKADIAGNIRDGAAIAFAHGLNVHFGLIEPK 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
           A +DV+MIAPK PGHTVR  Y +GGGVP L+AVHQ+ SG A D+ALSYA   GGGR+GII
Sbjct: 121 ASVDVVMIAPKGPGHTVRGEYQKGGGVPCLVAVHQDASGNALDLALSYACGVGGGRSGII 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ETNF+EE ETDLFGEQ VLCGG VELI+AGFETLVEAGYAPEMAYFECLHE+KLIVDLIY
Sbjct: 181 ETNFKEECETDLFGEQVVLCGGLVELIRAGFETLVEAGYAPEMAYFECLHEVKLIVDLIY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299
           EGGIANMNYSISN AE+GEYVTGPR++TE+TK  MK+ L DIQTG++   ++ E ++GA 
Sbjct: 241 EGGIANMNYSISNTAEWGEYVTGPRIITEDTKAEMKRVLKDIQTGKFTSEWMQEYRSGAA 300

Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
                RR+   HQIEEVGAKLRAMMPWI KNK+VD++KN
Sbjct: 301 RFKGIRRVNDSHQIEEVGAKLRAMMPWIGKNKLVDKAKN 339


Lambda     K      H
   0.316    0.133    0.379 

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: 436
Number of extensions: 16
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: 338
Length of database: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate SMc04346 SMc04346 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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.aa/TIGR00465.hmm
# target sequence database:        /tmp/gapView.8628.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.6e-132  424.7   1.5   1.1e-131  424.4   1.5    1.0  1  lcl|FitnessBrowser__Smeli:SMc04346  SMc04346 ketol-acid reductoisome


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04346  SMc04346 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.4   1.5  1.1e-131  1.1e-131       1     312 [.      14     327 ..      14     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.4 bits;  conditional E-value: 1.1e-131
                           TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 
                                         +k+kkvaiiGyGsqG+a+alnl+dsg  nv ++l++++a+ kkAe dGfkv+tv+ea++ adl+m+ +pDe+q +
  lcl|FitnessBrowser__Smeli:SMc04346  14 IKSKKVAIIGYGSQGRAHALNLKDSGAqNVAIALKSGSATAKKAEADGFKVMTVAEAAAWADLMMMATPDELQAD 88 
                                         689**********************9658********************************************** PP

                           TIGR00465  75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeake 149
                                          y+a+i+ ++++g+a+ f+HG n++f  i++++ vdvv++APKgpG++vR ey++g Gvp l+Av+qd++g+a +
  lcl|FitnessBrowser__Smeli:SMc04346  89 IYKADIAGNIRDGAAIAFAHGLNVHFGLIEPKASVDVVMIAPKGPGHTVRGEYQKGGGVPCLVAVHQDASGNALD 163
                                         *************************************************************************** PP

                           TIGR00465 150 iAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdl 224
                                          Al+yA ++Gg+r g++et FkeE+e+DLfGEq+vLcGgl +li+a+f+tLveaGy+pe+Ayfe++he+klivdl
  lcl|FitnessBrowser__Smeli:SMc04346 164 LALSYACGVGGGRSGIIETNFKEECETDLFGEQVVLCGGLVELIRAGFETLVEAGYAPEMAYFECLHEVKLIVDL 238
                                         *************************************************************************** PP

                           TIGR00465 225 lkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqe 298
                                         ++e+G+++m  ++sntA++g++ ++ +i++e +k+em+ +lk+iq+G+f++ew+ e + g+++f+ +r+ +  ++
  lcl|FitnessBrowser__Smeli:SMc04346 239 IYEGGIANMNYSISNTAEWGEYVTGpRIITEDTKAEMKRVLKDIQTGKFTSEWMQEYRSGAARFKGIRRVNDSHQ 313
                                         *************************9************************************************* PP

                           TIGR00465 299 iekvGkelralvka 312
                                         ie+vG +lra++++
  lcl|FitnessBrowser__Smeli:SMc04346 314 IEEVGAKLRAMMPW 327
                                         ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (339 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: 6.99
//
[ok]

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

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis