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.16423.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.50
//
[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:

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:

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:

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:

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