GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Pseudomonas fluorescens FW300-N2E2

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate Pf6N2E2_5176 Acetolactate synthase small subunit (EC 2.2.1.6)

Query= BRENDA::P00894
         (163 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5176
          Length = 163

 Score =  209 bits (533), Expect = 1e-59
 Identities = 101/162 (62%), Positives = 137/162 (84%), Gaps = 1/162 (0%)

Query: 1   MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60
           MR I+S+LLENE GALSRV+GLFSQR YNIESLTVAPT+DPTLSR+T+ TVG ++++EQI
Sbjct: 1   MRHIISLLLENEPGALSRVVGLFSQRNYNIESLTVAPTEDPTLSRLTLTTVGHDEIIEQI 60

Query: 61  EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120
            K L+KL++V+++ +L + AH+ERE+MLVK++A+G  R E+KR T+I+RGQI+DV+ S+Y
Sbjct: 61  TKNLNKLIEVVKLVDLSESAHIERELMLVKVKATGAQRAEIKRTTDIYRGQIVDVSASVY 120

Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIM 162
           TVQL GTS KLD+F+ SI   A I+E  RSGV G++RGDK++
Sbjct: 121 TVQLTGTSDKLDSFIQSI-GTASILETVRSGVTGIARGDKVL 161


Lambda     K      H
   0.318    0.136    0.360 

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: 125
Number of extensions: 2
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: 163
Length of database: 163
Length adjustment: 18
Effective length of query: 145
Effective length of database: 145
Effective search space:    21025
Effective search space used:    21025
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: 43 (21.2 bits)

Align candidate Pf6N2E2_5176 (Acetolactate synthase small subunit (EC 2.2.1.6))
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.3624386.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    1.3e-66  209.5   2.3    1.5e-66  209.3   2.3    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5176  Acetolactate synthase small subu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5176  Acetolactate synthase small subunit (EC 2.2.1.6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   2.3   1.5e-66   1.5e-66       1     158 []       1     158 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 1.5e-66
                                      TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekql 64 
                                                    ++h++s+l+enepG+Lsrv+Glf++r++niesltv+ te+++lsr+t+++ g+d+++eqi+k l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5176   1 MRHIISLLLENEPGALSRVVGLFSQRNYNIESLTVAPTEDPTLSRLTLTTVGHDEIIEQITKNL 64 
                                                    69************************************************************** PP

                                      TIGR00119  65 eklvdvlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgke 128
                                                    +kl++v+k +dl+es++++rel+lvkv+a+g +r+eik++t+i+rg++vDvs + ++v+l+g++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5176  65 NKLIEVVKLVDLSESAHIERELMLVKVKATGAQRAEIKRTTDIYRGQIVDVSASVYTVQLTGTS 128
                                                    **************************************************************** PP

                                      TIGR00119 129 dkisaflkllkefgikevarsGlvalsrge 158
                                                    dk+++f++++   +i+e +rsG+++++rg+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5176 129 DKLDSFIQSIGTASILETVRSGVTGIARGD 158
                                                    ****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (163 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: 12.38
//
[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