Alignments for a candidate for ilvI in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Cupriavidus basilensis 4G11

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate RR42_RS05440 RR42_RS05440 acetolactate synthase

Query= BRENDA::P00894
         (163 letters)



>FitnessBrowser__Cup4G11:RR42_RS05440
          Length = 163

 Score =  195 bits (496), Expect = 3e-55
 Identities = 98/163 (60%), Positives = 131/163 (80%), Gaps = 1/163 (0%)

Query: 1   MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60
           MR I+SVLLENE GALSRV+GLFS RGYNIE+LTVAPT+D +LSRMTI T G + ++EQI
Sbjct: 1   MRHIISVLLENEPGALSRVVGLFSARGYNIETLTVAPTEDASLSRMTIVTSGSDDIIEQI 60

Query: 61  EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120
            K L++LV+V++V +L +GAH+ERE+MLVK++A G  R+E+KR  +IFRG+IIDVT   Y
Sbjct: 61  TKHLNRLVEVVKVVDLTEGAHIERELMLVKVRAVGKEREEMKRTADIFRGRIIDVTEKTY 120

Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIMR 163
           T++L G  GKLDAFL +I D A I+E  R+G  G+ RG++I++
Sbjct: 121 TIELTGNGGKLDAFLDAI-DRAAILETVRTGGSGIGRGERILK 162


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: 113
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: 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 RR42_RS05440 RR42_RS05440 (acetolactate synthase)
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.12405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.8e-67  210.9   1.8    5.4e-67  210.8   1.8    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05440  RR42_RS05440 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05440  RR42_RS05440 acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   1.8   5.4e-67   5.4e-67       1     157 [.       1     157 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 5.4e-67
                                 TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 
                                               ++h++svl+enepG+Lsrv+Glf++rg+nie+ltv+ te++ lsrmtiv++g d+++eqi+k l++lv+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05440   1 MRHIISVLLENEPGALSRVVGLFSARGYNIETLTVAPTEDASLSRMTIVTSGSDDIIEQITKHLNRLVE 69 
                                               69******************************************************************* PP

                                 TIGR00119  70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138
                                               v+kv+dlte ++++rel+lvkv+a+g+er+e+k++++ifrgr++Dv+e+++++el+g+ +k++afl+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05440  70 VVKVVDLTEGAHIERELMLVKVRAVGKEREEMKRTADIFRGRIIDVTEKTYTIELTGNGGKLDAFLDAI 138
                                               ********************************************************************* PP

                                 TIGR00119 139 kefgikevarsGlvalsrg 157
                                                  +i+e +r+G  ++ rg
  lcl|FitnessBrowser__Cup4G11:RR42_RS05440 139 DRAAILETVRTGGSGIGRG 157
                                               ************9999997 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.30
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis