GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Shewanella oneidensis MR-1

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate 203314 SO4233 3-isopropylmalate dehydratase, small subunit (NCBI ptt file)

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__MR1:203314
          Length = 201

 Score =  244 bits (623), Expect = 8e-70
 Identities = 120/200 (60%), Positives = 145/200 (72%), Gaps = 1/200 (0%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           + FT HTGL V +D+AN+DTD IIPKQFL KVTR GFG HLF+DWR+LD+ G  PNPEF 
Sbjct: 2   QPFTCHTGLAVMIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGDVPNPEFT 61

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           LN P Y GASILLA+ENFGCGSSREHAPWAL D+G + +IAPSFADIFYGNS NN LLPV
Sbjct: 62  LNKPRYNGASILLAQENFGCGSSREHAPWALADFGLRAIIAPSFADIFYGNSINNGLLPV 121

Query: 123 TLSDAQVDELFALVKANPGIKFEVDL-EAQVVKAGDKTYSFKIDDFRRHCMLNGLDSIGL 181
            LS  +V +L   V +  G +  VDL   QV       +SF + +  RH +LNGLD+IGL
Sbjct: 122 KLSANEVRQLMDEVASEEGAQITVDLTTCQVTSPSGAQFSFSLAESARHKLLNGLDAIGL 181

Query: 182 TLQHEDAIAAYENKQPAFMR 201
           TL H   I+ YE++ P++ R
Sbjct: 182 TLSHGAQISEYESQIPSWRR 201


Lambda     K      H
   0.321    0.138    0.416 

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: 166
Number of extensions: 4
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: 201
Length of database: 201
Length adjustment: 21
Effective length of query: 180
Effective length of database: 180
Effective search space:    32400
Effective search space used:    32400
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate 203314 SO4233 (3-isopropylmalate dehydratase, small subunit (NCBI ptt file))
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.24866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    5.8e-86  273.2   0.0    6.5e-86  273.0   0.0    1.0  1  lcl|FitnessBrowser__MR1:203314  SO4233 3-isopropylmalate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203314  SO4233 3-isopropylmalate dehydratase, small subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.0   0.0   6.5e-86   6.5e-86       1     188 []       1     189 [.       1     189 [. 0.99

  Alignments for each domain:
  == domain 1  score: 273.0 bits;  conditional E-value: 6.5e-86
                       TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillarenf 79 
                                     m++f  +tGl+v +d an+dtd+iipkqfl k++r Gfg hlf++wryld+ G+ pnpef ln p+y+gasilla+enf
  lcl|FitnessBrowser__MR1:203314   1 MQPFTCHTGLAVMIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGDVPNPEFTLNKPRYNGASILLAQENF 79 
                                     89***************************************************************************** PP

                       TIGR00171  80 GcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqkvkdsegk 157
                                     GcGssrehapwal+d+G++ iiapsfadify+ns++ngllp++ls +ev++l+  v+ ++g ++tvdl + +v++  g 
  lcl|FitnessBrowser__MR1:203314  80 GCGSSREHAPWALADFGLRAIIAPSFADIFYGNSINNGLLPVKLSANEVRQLMDEVAsEEGAQITVDLTTCQVTSPSGA 158
                                     ********************************************************9899******************* PP

                       TIGR00171 158 vysfeidefrkhcllnGldeigltlqkedei 188
                                     + sf + e  +h llnGld igltl +  +i
  lcl|FitnessBrowser__MR1:203314 159 QFSFSLAESARHKLLNGLDAIGLTLSHGAQI 189
                                     *************************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (201 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: 00:00:00.00
# Mc/sec: 5.77
//
[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