Alignments for a candidate for proB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Pedobacter sp. GW460-11-11-14-LB5

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate CA265_RS20855 CA265_RS20855 glutamate 5-kinase

Query= reanno::Pedo557:CA265_RS20855
         (359 letters)



>FitnessBrowser__Pedo557:CA265_RS20855
          Length = 359

 Score =  689 bits (1778), Expect = 0.0
 Identities = 359/359 (100%), Positives = 359/359 (100%)

Query: 1   MKLGYKKIVVKVGSNVITQANGLPDEGRIKHLVNQLADIKKQGIEVILVSSGAVASGRSL 60
           MKLGYKKIVVKVGSNVITQANGLPDEGRIKHLVNQLADIKKQGIEVILVSSGAVASGRSL
Sbjct: 1   MKLGYKKIVVKVGSNVITQANGLPDEGRIKHLVNQLADIKKQGIEVILVSSGAVASGRSL 60

Query: 61  IKVSEKQDAVTTRQLLAAIGQVKLINTYANFFAAHAIQCAQVLVTKEDFRDRAHYLNMKN 120
           IKVSEKQDAVTTRQLLAAIGQVKLINTYANFFAAHAIQCAQVLVTKEDFRDRAHYLNMKN
Sbjct: 61  IKVSEKQDAVTTRQLLAAIGQVKLINTYANFFAAHAIQCAQVLVTKEDFRDRAHYLNMKN 120

Query: 121 CLQILLQNEVIPVVNENDVVSVTELMFTDNDELAGLIASMLNADALIILSNVNGIYNGDP 180
           CLQILLQNEVIPVVNENDVVSVTELMFTDNDELAGLIASMLNADALIILSNVNGIYNGDP
Sbjct: 121 CLQILLQNEVIPVVNENDVVSVTELMFTDNDELAGLIASMLNADALIILSNVNGIYNGDP 180

Query: 181 KVEGSAVIEEINGSVANLASFIQTGKSQFGRGGMITKSTMAQKVAKLGITVHIANGTKDN 240
           KVEGSAVIEEINGSVANLASFIQTGKSQFGRGGMITKSTMAQKVAKLGITVHIANGTKDN
Sbjct: 181 KVEGSAVIEEINGSVANLASFIQTGKSQFGRGGMITKSTMAQKVAKLGITVHIANGTKDN 240

Query: 241 VLTSLLNNELVHTRFVPEKSKSGKKKWIAHSETAATGVVKLNDGAKTVLTSSKATSLLPV 300
           VLTSLLNNELVHTRFVPEKSKSGKKKWIAHSETAATGVVKLNDGAKTVLTSSKATSLLPV
Sbjct: 241 VLTSLLNNELVHTRFVPEKSKSGKKKWIAHSETAATGVVKLNDGAKTVLTSSKATSLLPV 300

Query: 301 GIIEIQTDFLKGDIIKIVDEKNNLIGLGIAEYGSDKARERIGQKKQKALVHYDYFYSAI 359
           GIIEIQTDFLKGDIIKIVDEKNNLIGLGIAEYGSDKARERIGQKKQKALVHYDYFYSAI
Sbjct: 301 GIIEIQTDFLKGDIIKIVDEKNNLIGLGIAEYGSDKARERIGQKKQKALVHYDYFYSAI 359


Lambda     K      H
   0.316    0.133    0.358 

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: 611
Number of extensions: 11
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: 359
Length of database: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
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: 49 (23.5 bits)

Align candidate CA265_RS20855 CA265_RS20855 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.1533923.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    6.1e-97  310.9  12.6    6.8e-97  310.8  12.6    1.0  1  FitnessBrowser__Pedo557:CA265_RS20855  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Pedo557:CA265_RS20855  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.8  12.6   6.8e-97   6.8e-97       1     344 [.       6     349 ..       6     359 .] 0.94

  Alignments for each domain:
  == domain 1  score: 310.8 bits;  conditional E-value: 6.8e-97
                              TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQala 72 
                                            k+iVvK+Gs+++t+ +g +++ ++++lv+q+a +kk+G ev++vsSGava+G + + ++e++  ++++Q+la
  FitnessBrowser__Pedo557:CA265_RS20855   6 KKIVVKVGSNVITQANGLPDEGRIKHLVNQLADIKKQGIEVILVSSGAVASGRSLIKVSEKQDAVTTRQLLA 77 
                                            68********************************************************************** PP

                              TIGR01027  73 aVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGD 144
                                            a+GQ++L+++y + f+ + ++ aQ+L t++d+++r +ylN +n l+ ll+++v+p+vNEND v+v+e+ f D
  FitnessBrowser__Pedo557:CA265_RS20855  78 AIGQVKLINTYANFFAAHAIQCAQVLVTKEDFRDRAHYLNMKNCLQILLQNEVIPVVNENDVVSVTELMFTD 149
                                            ************************************************************************ PP

                              TIGR01027 145 NDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKlea 216
                                            ND+L+ l+a++++Ad+L++l++v+g+y+ dp+ +  A +iee++   ++l ++  ++ s++G GGm tK + 
  FitnessBrowser__Pedo557:CA265_RS20855 150 NDELAGLIASMLNADALIILSNVNGIYNGDPKVEGSA-VIEEINGSVANLASFIQTGKSQFGRGGMITKSTM 220
                                            *******************************888776.7899998888888777777789************ PP

                              TIGR01027 217 aelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaas.eakGkiivdegaeealle 287
                                            a+  +++g+ v ia+g+k + +++ll+++ v+t f ++k+  + +k+wi++ + +a+G + +++ga++ l++
  FitnessBrowser__Pedo557:CA265_RS20855 221 AQKVAKLGITVHIANGTKDNVLTSLLNNELVHTRFVPEKS-KSGKKKWIAHSEtAATGVVKLNDGAKTVLTS 291
                                            *************************************988.5778899999761578************987 PP

                              TIGR01027 288 .kgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeie 344
                                             k +sLlp+g++e++ +F +g++++i++e+ + ig g ++y s++ ++  g+k+++  
  FitnessBrowser__Pedo557:CA265_RS20855 292 sKATSLLPVGIIEIQTDFLKGDIIKIVDEKNNLIGLGIAEYGSDKARERIGQKKQKAL 349
                                            25678******************************************99999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (359 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: 27.14
//
[ok]

This GapMind analysis is from Jul 25 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:

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
the source code
instructions for running GapMind on your computer
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