GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Synechococcus elongatus PCC 7942

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate Synpcc7942_2434 Synpcc7942_2434 acetolactate synthase 3 regulatory subunit

Query= BRENDA::P9WKJ3
         (168 letters)



>FitnessBrowser__SynE:Synpcc7942_2434
          Length = 172

 Score =  163 bits (413), Expect = 1e-45
 Identities = 85/153 (55%), Positives = 117/153 (76%)

Query: 7   TLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITKQ 66
           TLSVLVED+ GVL R+A LF+RR FNIESLAVG  E    SR+T+VV  +D  +EQITKQ
Sbjct: 4   TLSVLVEDEAGVLTRIAGLFARRSFNIESLAVGPAEQVGISRITMVVQGDDREIEQITKQ 63

Query: 67  LNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTVE 126
           L KLINV+K+ +  +   V REL LIKV A++ +RS+++E V +FRA V+DV+ +SL VE
Sbjct: 64  LYKLINVLKVQDISEVPCVERELMLIKVNANSSNRSEILELVQIFRARVVDVAEDSLIVE 123

Query: 127 ATGNRGKLEALLRVLEPFGIREIAQSGMVSLSR 159
             G+ GK+ A+++VL+ FGIREI+++G V+L+R
Sbjct: 124 VVGDPGKMVAIVQVLQRFGIREISRTGKVALTR 156


Lambda     K      H
   0.315    0.131    0.347 

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: 99
Number of extensions: 3
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: 168
Length of database: 172
Length adjustment: 18
Effective length of query: 150
Effective length of database: 154
Effective search space:    23100
Effective search space used:    23100
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: 43 (21.2 bits)

Align candidate Synpcc7942_2434 Synpcc7942_2434 (acetolactate synthase 3 regulatory subunit)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))

# 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/TIGR00119.hmm
# target sequence database:        /tmp/gapView.3627314.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00119  [M=158]
Accession:   TIGR00119
Description: acolac_sm: acetolactate synthase, 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.5e-69  218.3   7.9    2.9e-69  218.2   7.9    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2434  Synpcc7942_2434 acetolactate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2434  Synpcc7942_2434 acetolactate synthase 3 regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.2   7.9   2.9e-69   2.9e-69       1     157 [.       1     157 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 2.9e-69
                                 TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 
                                               +k++lsvlve+e+GvL+r++Glfarr+fniesl+vg +e+ ++sr+t+vv+gdd+ +eqi+kql+kl++
  lcl|FitnessBrowser__SynE:Synpcc7942_2434   1 MKRTLSVLVEDEAGVLTRIAGLFARRSFNIESLAVGPAEQVGISRITMVVQGDDREIEQITKQLYKLIN 69 
                                               699****************************************************************** PP

                                 TIGR00119  70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138
                                               vlkv+d++e  +v+rel+l+kv+a++++r+ei el++ifr+rvvDv+edslive++g+++k+ a++++l
  lcl|FitnessBrowser__SynE:Synpcc7942_2434  70 VLKVQDISEVPCVERELMLIKVNANSSNRSEILELVQIFRARVVDVAEDSLIVEVVGDPGKMVAIVQVL 138
                                               ********************************************************************* PP

                                 TIGR00119 139 kefgikevarsGlvalsrg 157
                                               + fgi+e++r+G+val+r+
  lcl|FitnessBrowser__SynE:Synpcc7942_2434 139 QRFGIREISRTGKVALTRE 157
                                               *****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (172 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: 9.11
//
[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