GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate AZOBR_RS15560 AZOBR_RS15560 isopropylmalate isomerase

Query= SwissProt::Q1MA52
         (202 letters)



>FitnessBrowser__azobra:AZOBR_RS15560
          Length = 198

 Score =  177 bits (449), Expect = 1e-49
 Identities = 90/200 (45%), Positives = 123/200 (61%), Gaps = 7/200 (3%)

Query: 1   MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60
           MD FV LT  A PL + N+DTD ++P  +LK  +  G G  LF + R        P F L
Sbjct: 1   MDPFVTLTAPAVPLDIANIDTDQLLPARFLKKPRSAGYGNFLFHDER-------KPGFPL 53

Query: 61  NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120
           + PAY  A++LV+  NFGCGSSRE A +AL+D G RCV++ SF DIF  N  KNG+L I 
Sbjct: 54  DDPAYAGARVLVSDRNFGCGSSREGAVYALVDGGFRCVVAPSFGDIFAANAAKNGLLTIT 113

Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180
           + +E + +L         A +TVDL    ++GPDG  + F +D FK+ CL+ GLDD+ LT
Sbjct: 114 LPEETVAELRRQLQEAPGAAVTVDLPAQTLSGPDGQPLPFAIDPFKKECLIEGLDDVALT 173

Query: 181 LEKGKAIDSFEKKNAASHPW 200
           L    AID+F++ +AA+ PW
Sbjct: 174 LRHQDAIDAFDRADAAARPW 193


Lambda     K      H
   0.319    0.140    0.419 

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: 135
Number of extensions: 6
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: 202
Length of database: 198
Length adjustment: 21
Effective length of query: 181
Effective length of database: 177
Effective search space:    32037
Effective search space used:    32037
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate AZOBR_RS15560 AZOBR_RS15560 (isopropylmalate isomerase)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

# 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/TIGR00171.hmm
# target sequence database:        /tmp/gapView.2996454.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00171  [M=188]
Accession:   TIGR00171
Description: leuD: 3-isopropylmalate dehydratase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.9e-57  178.0   0.0    1.2e-56  177.6   0.0    1.1  1  lcl|FitnessBrowser__azobra:AZOBR_RS15560  AZOBR_RS15560 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS15560  AZOBR_RS15560 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.6   0.0   1.2e-56   1.2e-56       1     188 []       1     180 [.       1     180 [. 0.98

  Alignments for each domain:
  == domain 1  score: 177.6 bits;  conditional E-value: 1.2e-56
                                 TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 
                                               m++f++lt  +vpld an+dtd+++p +flkk +  G+g++lf++ r          p f l+ p y g
  lcl|FitnessBrowser__azobra:AZOBR_RS15560   1 MDPFVTLTAPAVPLDIANIDTDQLLPARFLKKPRSAGYGNFLFHDERK---------PGFPLDDPAYAG 60 
                                               899*****************************************9765.........88********** PP

                                 TIGR00171  70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.n 137
                                               a +l++  nfGcGssre a +al d Gf+ ++apsf+dif  n+ kngll i l+ee+v el  +++  
  lcl|FitnessBrowser__azobra:AZOBR_RS15560  61 ARVLVSDRNFGCGSSREGAVYALVDGGFRCVVAPSFGDIFAANAAKNGLLTITLPEETVAELRRQLQeA 129
                                               ***************************************************************999979 PP

                                 TIGR00171 138 kglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                               +g  +tvdl+aq++   +g+   f id+f+k+cl++Gld+++ltl+++d+i
  lcl|FitnessBrowser__azobra:AZOBR_RS15560 130 PGAAVTVDLPAQTLSGPDGQPLPFAIDPFKKECLIEGLDDVALTLRHQDAI 180
                                               9************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (198 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: 11.77
//
[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