Alignments for a candidate for proB in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Acidovorax sp. GW101-3H11

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Ac3H11_4771 Glutamate 5-kinase (EC 2.7.2.11)

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4771
          Length = 384

 Score =  280 bits (715), Expect = 6e-80
 Identities = 163/370 (44%), Positives = 223/370 (60%), Gaps = 5/370 (1%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQL----HAAGHRIVIVTSGAIAAG 56
           + D++ +VVK+G+S++T   R L+   I E  RQ A L          +V+V+SGAIA G
Sbjct: 10  LRDARRIVVKVGSSLVTNEGRGLDETAIGEWSRQLAALVRGDGGVAREVVMVSSGAIAEG 69

Query: 57  REHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLN 116
            + LG+   P  I   Q  AAVGQ  L Q++E      G+   Q+LLT AD+ DRER+LN
Sbjct: 70  MKRLGWTTRPQEIHELQAAAAVGQMGLAQMYETKLREEGMGSAQVLLTHADLADRERYLN 129

Query: 117 ARDTLRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYT 176
           AR TL  LL   +VPVINEND V   EIK GDND L AL A L  AD L++LTDQKGLYT
Sbjct: 130 ARSTLLTLLRLGVVPVINENDTVVNDEIKFGDNDTLGALVANLVEADALIILTDQKGLYT 189

Query: 177 ADPRSNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAG 236
           ADPR +P A+ + +    D AL A+AG + S +G GGM TK+ AA  A  +G  T+IA G
Sbjct: 190 ADPRRDPAAQFVHEAKAGDLALEAMAGGAGSSIGRGGMITKILAAKRAAGSGASTVIAWG 249

Query: 237 SKPGVIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSL 295
            +P V+  ++ G S+GTL  AQ    + RK+W+       G + VD GA A + + G SL
Sbjct: 250 REPDVLLRLVGGESLGTLLVAQTQKKQARKQWMADHLQLRGSVVVDAGAAAKVRDEGKSL 309

Query: 296 LPKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYG 355
           LP G+ +V G+FSRG+VI + +  G +IA G++ Y +   R +    S E + +LGY   
Sbjct: 310 LPIGMTAVEGDFSRGDVIAVRDASGVEIARGLANYAAAEARLLCRKPSAEFEKLLGYVAE 369

Query: 356 PVAVHRDDMI 365
           P  VHRD+++
Sbjct: 370 PEMVHRDNLV 379


Lambda     K      H
   0.318    0.135    0.384 

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: 347
Number of extensions: 16
Number of successful extensions: 3
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: 367
Length of database: 384
Length adjustment: 30
Effective length of query: 337
Effective length of database: 354
Effective search space:   119298
Effective search space used:   119298
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: 50 (23.9 bits)

Align candidate Ac3H11_4771 (Glutamate 5-kinase (EC 2.7.2.11))
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.29090.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.5e-126  406.8   2.0   5.2e-126  406.6   2.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771  Glutamate 5-kinase (EC 2.7.2.11)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771  Glutamate 5-kinase (EC 2.7.2.11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.6   2.0  5.2e-126  5.2e-126       1     362 [.      14     379 ..      14     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 406.6 bits;  conditional E-value: 5.2e-126
                                        TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkk.aG...hevvivsSGavaaGleaLgl 58 
                                                      +riVvK+Gss++t+e + l+++ + e  +q+a+l + +G   +evv+vsSGa+a G+++Lg 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771  14 RRIVVKVGSSLVTNEGRGLDETAIGEWSRQLAALVRgDGgvaREVVMVSSGAIAEGMKRLGW 75 
                                                      59*************999***************97633334489****************** PP

                                        TIGR01027  59 perpkklaekQalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleel 120
                                                      ++rp++++e Qa+aaVGQ  L + ye+++ + g+ +aQ+LLt+adl++rerylNar+tl +l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771  76 TTRPQEIHELQAAAAVGQMGLAQMYETKLREEGMGSAQVLLTHADLADRERYLNARSTLLTL 137
                                                      ************************************************************** PP

                                        TIGR01027 121 lelgvvpivNENDtvaveeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAk 182
                                                      l lgvvp++NENDtv  +eikfGDNDtL alva+lveAd+L++ltd++gLy+adpr++p A+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771 138 LRLGVVPVINENDTVVNDEIKFGDNDTLGALVANLVEADALIILTDQKGLYTADPRRDPAAQ 199
                                                      ************************************************************** PP

                                        TIGR01027 183 lieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasgekpekiadlled 244
                                                      +++e ++ + +l+a+ag++gss+G GGm tK+ aa+ A+ +g  ++ia g++p+ +++l+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771 200 FVHEAKAGDLALEAMAGGAGSSIGRGGMITKILAAKRAAGSGASTVIAWGREPDVLLRLVGG 261
                                                      ************************************************************** PP

                                        TIGR01027 245 aavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsr 306
                                                      +++gtl+ a+++k ++rkqw++ +++ +G+++vd+ga+++++++gksLlp g+++veg+Fsr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771 262 ESLGTLLVAQTQKKQARKQWMADHLQLRGSVVVDAGAAAKVRDEGKSLLPIGMTAVEGDFSR 323
                                                      ************************************************************** PP

                                        TIGR01027 307 gevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                                      g+v+ +++ +g ei++gl+ny ++e + +++++s+e e++Lgy  + e vhrdnlv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4771 324 GDVIAVRDASGVEIARGLANYAAAEARLLCRKPSAEFEKLLGYVAEPEMVHRDNLV 379
                                                      ******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (384 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.77
//
[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:

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