GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Flavobacterium glycines Gm-149

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_066328411.1 BLR17_RS00955 3-isopropylmalate dehydratase small subunit

Query= uniprot:A0A1X9Z766
         (195 letters)



>NCBI__GCF_900100165.1:WP_066328411.1
          Length = 198

 Score =  265 bits (677), Expect = 4e-76
 Identities = 125/190 (65%), Positives = 155/190 (81%)

Query: 3   KFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRYENDNQPKADFVMNN 62
           KF  LTS+ VPL IEN+DTDQIIPARFLKAT REGFG+NLFRDWRY  D+ PKADFV+NN
Sbjct: 5   KFNILTSSAVPLPIENVDTDQIIPARFLKATKREGFGDNLFRDWRYNGDDTPKADFVLNN 64

Query: 63  PTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQVSD 122
           PTYSG++LV GKNFG GSSREHAAWA+ D GF AV+SSFFADIFKGN LN G+LP+QVS 
Sbjct: 65  PTYSGKILVGGKNFGSGSSREHAAWAVYDYGFRAVVSSFFADIFKGNCLNIGVLPVQVSP 124

Query: 123 EFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFILN 182
           EF  +IF A++ +P + LE++L  QT+T+  TG +ESF+IN YKK+ ++NG+DDID++ +
Sbjct: 125 EFSDKIFAAIEADPNTELEINLPEQTITLKATGEKESFDINGYKKNNMLNGFDDIDYLQS 184

Query: 183 QKQLIEEFEE 192
            K+ I  F E
Sbjct: 185 VKEEIVSFAE 194


Lambda     K      H
   0.318    0.135    0.393 

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: 194
Number of extensions: 5
Number of successful extensions: 1
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: 195
Length of database: 198
Length adjustment: 20
Effective length of query: 175
Effective length of database: 178
Effective search space:    31150
Effective search space used:    31150
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: 45 (21.9 bits)

Align candidate WP_066328411.1 BLR17_RS00955 (3-isopropylmalate dehydratase small subunit)
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.2967270.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-57  179.8   0.1    3.3e-57  179.4   0.1    1.0  1  NCBI__GCF_900100165.1:WP_066328411.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066328411.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   0.1   3.3e-57   3.3e-57       3     181 ..       5     182 ..       3     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 3.3e-57
                             TIGR00171   3 efkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasilla 75 
                                           +f  lt  +vpl   nvdtd+iip +flk+ kr Gfg +lf +wry  ++   p+++fvln p+y g +il+ 
  NCBI__GCF_900100165.1:WP_066328411.1   5 KFNILTSSAVPLPIENVDTDQIIPARFLKATKREGFGDNLFRDWRYNGDD--TPKADFVLNNPTYSG-KILVG 74 
                                           57788999**************************************6444..499**********97.7**** PP

                             TIGR00171  76 renfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdle 147
                                           ++nfG Gssreha wa+ dyGf+ +++  fadif +n+++ g+lp+++s e  ++++a ++ ++ ++l+++l+
  NCBI__GCF_900100165.1:WP_066328411.1  75 GKNFGSGSSREHAAWAVYDYGFRAVVSSFFADIFKGNCLNIGVLPVQVSPEFSDKIFAAIEaDPNTELEINLP 147
                                           ************************************************************98999******** PP

                             TIGR00171 148 aqkvk.dsegkvysfeidefrkhcllnGldeiglt 181
                                           +q+++ ++ g++ sf+i+ ++k+ +lnG+d+i   
  NCBI__GCF_900100165.1:WP_066328411.1 148 EQTITlKATGEKESFDINGYKKNNMLNGFDDIDYL 182
                                           ***9735778**********************854 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: 15.93
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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