GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Azospirillum brasilense Sp245

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate AZOBR_RS06570 AZOBR_RS06570 ketol-acid reductoisomerase

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



>FitnessBrowser__azobra:AZOBR_RS06570
          Length = 339

 Score =  464 bits (1194), Expect = e-135
 Identities = 230/339 (67%), Positives = 271/339 (79%), Gaps = 1/339 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59
           M+V+YD+DAD++LIKGK V I+GYGSQGHAHA NL+DSGV +V + LR   A+  KA  A
Sbjct: 1   MRVYYDRDADVNLIKGKKVVIVGYGSQGHAHANNLRDSGVKDVRIALRPGSATIKKAEAA 60

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           G  V    EA   ADVVMIL PDE  AD+Y++++  N+KEGAALAFAHG NVH+  + PR
Sbjct: 61  GFTVMAPGEAAAWADVVMILTPDELQADLYRDDLAKNLKEGAALAFAHGLNVHFNLIEPR 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
           ADLDV MIAPK PGHTVR  Y +GGGVP L+AVHQN SG   DIALSYA+A GGGRAGII
Sbjct: 121 ADLDVFMIAPKGPGHTVRGEYQRGGGVPCLVAVHQNASGNGLDIALSYASAIGGGRAGII 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ET F+EE ETDLFGEQAVLCGG  ELIKAG+ETL EAGYAPEMAYFECLHE+KLIVDL+Y
Sbjct: 181 ETTFKEECETDLFGEQAVLCGGLTELIKAGYETLTEAGYAPEMAYFECLHEVKLIVDLMY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299
           EGG+ANM YSISN AEYG+Y TGPR++T ETK  MK+ L DIQTG + + ++LE KAG P
Sbjct: 241 EGGMANMRYSISNTAEYGDYKTGPRIITPETKAEMKRVLEDIQTGRFVRDWMLECKAGQP 300

Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           +  + RR  AEH IE+VG KLRAMMPWIA+ ++VD+SKN
Sbjct: 301 SFKATRRRNAEHSIEQVGEKLRAMMPWIAERRLVDKSKN 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: 449
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 AZOBR_RS06570 AZOBR_RS06570 (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.30483.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-137  441.9   0.1   6.2e-137  441.7   0.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS06570  AZOBR_RS06570 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS06570  AZOBR_RS06570 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.7   0.1  6.2e-137  6.2e-137       1     312 [.      14     327 ..      14     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 441.7 bits;  conditional E-value: 6.2e-137
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlp 68 
                                               +kgkkv+i+GyGsqG+a+a nlrdsg+ +v+++lr+++a++kkAe  Gf v+   ea++ ad++miL+p
  lcl|FitnessBrowser__azobra:AZOBR_RS06570  14 IKGKKVVIVGYGSQGHAHANNLRDSGVkDVRIALRPGSATIKKAEAAGFTVMAPGEAAAWADVVMILTP 82 
                                               689************************67**************************************** PP

                                 TIGR00465  69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsli 137
                                               De+q + y+ +++ +lkeg+al f+HG n++f+ i++++d+dv+++APKgpG++vR ey++g Gvp l+
  lcl|FitnessBrowser__azobra:AZOBR_RS06570  83 DELQADLYRDDLAKNLKEGAALAFAHGLNVHFNLIEPRADLDVFMIAPKGPGHTVRGEYQRGGGVPCLV 151
                                               ********************************************************************* PP

                                 TIGR00465 138 AveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyq 206
                                               Av+q+++g++ +iAl+yA aiGg+rag++ettFkeE+e+DLfGEqavLcGgl++lika+++tL+eaGy+
  lcl|FitnessBrowser__azobra:AZOBR_RS06570 152 AVHQNASGNGLDIALSYASAIGGGRAGIIETTFKEECETDLFGEQAVLCGGLTELIKAGYETLTEAGYA 220
                                               ********************************************************************* PP

                                 TIGR00465 207 pelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefak 274
                                               pe+Ayfe++he+klivdl++e+G+++mr ++sntA++g+++++ +i++ e+k+em+ +l++iq+G+f +
  lcl|FitnessBrowser__azobra:AZOBR_RS06570 221 PEMAYFECLHEVKLIVDLMYEGGMANMRYSISNTAEYGDYKTGpRIITPETKAEMKRVLEDIQTGRFVR 289
                                               ********************************************************************* PP

                                 TIGR00465 275 ewalekeagkpafeearkkekeqeiekvGkelralvka 312
                                               +w+le +ag+p+f+++r+++ e++ie+vG++lra++++
  lcl|FitnessBrowser__azobra:AZOBR_RS06570 290 DWMLECKAGQPSFKATRRRNAEHSIEQVGEKLRAMMPW 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: 00:00:00.00
# Mc/sec: 11.01
//
[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