Alignments for a candidate for proB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Herbaspirillum seropedicae SmR1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate HSERO_RS01815 HSERO_RS01815 gamma-glutamyl kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__HerbieS:HSERO_RS01815
          Length = 372

 Score =  299 bits (766), Expect = 7e-86
 Identities = 165/363 (45%), Positives = 224/363 (61%), Gaps = 1/363 (0%)

Query: 4   SQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYP 63
           ++ L++K+G+S++T   + L+   I     Q AQL A G  +V+V+SGA+A G + LG+ 
Sbjct: 8   AKRLIIKVGSSLVTNDGKGLDANAIARWAEQIAQLRALGKEVVLVSSGAVAEGMQRLGFE 67

Query: 64  ELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRA 123
           + P  I   Q  AAVGQ  L Q++E  F  + +H  Q+LLT AD+ DRER+LNAR TL A
Sbjct: 68  KRPTGIHHLQACAAVGQMGLAQIYETSFRKHDLHTAQVLLTHADLADRERYLNARSTLFA 127

Query: 124 LLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNP 183
           LL   +VPVINEND V T EIK GDND L AL A L  A+ L++LTDQ GL+TADPR +P
Sbjct: 128 LLQLGVVPVINENDTVVTDEIKFGDNDTLGALVANLIEAEALIILTDQPGLFTADPRKDP 187

Query: 184 QAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIG 243
            A LI +    D +L  IAG + +G+G GGM TK+ AA  A  +G  T+IA G +  V+ 
Sbjct: 188 TATLISEARAGDPSLELIAGGTGTGIGRGGMLTKILAAKRAATSGAHTVIAWGREEQVLT 247

Query: 244 DVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKGIKS 302
            +  G ++GT  +A+   L  RK+W+      AG + +D GA   +   G SLLP G+  
Sbjct: 248 RLAAGEAIGTQLNAETAQLTARKQWMADHLKTAGRVVLDAGAVQKLSLEGKSLLPIGVVE 307

Query: 303 VTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRD 362
           V+G F RG+VI   +  GR IA G+S YNS   RRI  H S EI AILG+   P  VHRD
Sbjct: 308 VSGEFGRGDVITCVDENGRAIARGMSNYNSSDARRIIRHPSSEIQAILGFVEEPELVHRD 367

Query: 363 DMI 365
           +++
Sbjct: 368 NLV 370


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: 362
Number of extensions: 17
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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: 49 (23.5 bits)

Align candidate HSERO_RS01815 HSERO_RS01815 (gamma-glutamyl 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.29577.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.2e-134  435.0   1.6   1.4e-134  434.8   1.6    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS01815  HSERO_RS01815 gamma-glutamyl kin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS01815  HSERO_RS01815 gamma-glutamyl kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.8   1.6  1.4e-134  1.4e-134       1     362 [.       9     370 ..       9     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 434.8 bits;  conditional E-value: 1.4e-134
                                  TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaek 68 
                                                kr+++K+Gss++t++ + l+++ +a+ +eq+a+l++ G+evv+vsSGava G+++Lg+++rp+ +++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS01815   9 KRLIIKVGSSLVTNDGKGLDANAIARWAEQIAQLRALGKEVVLVSSGAVAEGMQRLGFEKRPTGIHHL 76 
                                                699************999************************************************** PP

                                  TIGR01027  69 QalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtva 136
                                                Qa aaVGQ  L + ye++f +++l++aQ+LLt+adl++rerylNar+tl +ll+lgvvp++NENDtv 
  lcl|FitnessBrowser__HerbieS:HSERO_RS01815  77 QACAAVGQMGLAQIYETSFRKHDLHTAQVLLTHADLADRERYLNARSTLFALLQLGVVPVINENDTVV 144
                                                ******************************************************************** PP

                                  TIGR01027 137 veeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgss 204
                                                ++eikfGDNDtL alva+l+eA++L++ltd+ gL++adpr++p+A+li+e ++ + +l+ +ag++g+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS01815 145 TDEIKFGDNDTLGALVANLIEAEALIILTDQPGLFTADPRKDPTATLISEARAGDPSLELIAGGTGTG 212
                                                ******************************************************************** PP

                                  TIGR01027 205 vGTGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseak 272
                                                +G GGm tK+ aa+ A+++g +++ia g++++ +++l++++a+gt+++a++++l +rkqw++ +++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01815 213 IGRGGMLTKILAAKRAATSGAHTVIAWGREEQVLTRLAAGEAIGTQLNAETAQLTARKQWMADHLKTA 280
                                                ******************************************************************** PP

                                  TIGR01027 273 GkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglks 340
                                                G++++d+ga+++l+ +gksLlp gvvev+g+F rg+v+++++e+g+ i++g++ny+s++ ++i +++s
  lcl|FitnessBrowser__HerbieS:HSERO_RS01815 281 GRVVLDAGAVQKLSLEGKSLLPIGVVEVSGEFGRGDVITCVDENGRAIARGMSNYNSSDARRIIRHPS 348
                                                ******************************************************************** PP

                                  TIGR01027 341 eeiedvLgyekkeevvhrdnlv 362
                                                +ei+++Lg+ ++ e vhrdnlv
  lcl|FitnessBrowser__HerbieS:HSERO_RS01815 349 SEIQAILGFVEEPELVHRDNLV 370
                                                ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (372 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: 00:00:00.01
# Mc/sec: 10.62
//
[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