Alignments for a candidate for proB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Shewanella oneidensis MR-1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 200301 SO1121 glutamate 5-kinase (NCBI ptt file)

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__MR1:200301
          Length = 372

 Score =  443 bits (1139), Expect = e-129
 Identities = 228/360 (63%), Positives = 280/360 (77%), Gaps = 1/360 (0%)

Query: 7   LVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELP 66
           +VVKLGTSVLT GS++L++AH+VEL RQ A L  +G  +V+ TSGAIAAGREHL YP LP
Sbjct: 11  VVVKLGTSVLTSGSKQLDKAHMVELARQMAALMRSGVEVVLCTSGAIAAGREHLQYPALP 70

Query: 67  ATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLD 126
            T+A+KQLLAAVGQS+LI  W QLFSIYG+HVGQ+LLTRAD+ DRER+LNARDTL ALL 
Sbjct: 71  DTMANKQLLAAVGQSQLILAWAQLFSIYGLHVGQLLLTRADLHDRERYLNARDTLNALLA 130

Query: 127 NNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAE 186
           NNI+P+INENDAVAT EIKVGDNDNLSA AA+L  AD L+LLTDQKGL+ ADPR+NP A+
Sbjct: 131 NNIIPIINENDAVATNEIKVGDNDNLSARAALLCDADLLILLTDQKGLFDADPRTNPNAK 190

Query: 187 LIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVM 246
           LI  V  IDD+LR +AG SVSGLGTGGMSTKL+AAD+A RAGI+ +IA+G  P VI  V+
Sbjct: 191 LISQVEKIDDSLRLLAGGSVSGLGTGGMSTKLEAADIARRAGIEVVIASGHHPDVIKKVV 250

Query: 247 EGISVGTLFHAQATPLENRKRWIFGAPPA-GEITVDEGATAAILERGSSLLPKGIKSVTG 305
              S+GT F A   PLE+RK+WI   P A G + +D GA  A+ E+G SLL KGI  V G
Sbjct: 251 AKESIGTHFSAIENPLESRKQWILAGPAAQGSLVLDAGAVKAVTEKGRSLLSKGIIGVKG 310

Query: 306 NFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
            F RG  +++ +  G+ IA G++RY  +AL  IAG HS EI+++LGY+YG   VHR+DM+
Sbjct: 311 EFERGATLQLVDQNGKIIARGITRYCGEALGLIAGKHSDEIESVLGYDYGDAIVHRNDMV 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: 403
Number of extensions: 10
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 200301 SO1121 (glutamate 5-kinase (NCBI ptt file))
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.19419.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.5e-147  476.2   3.0     4e-147  476.0   3.0    1.0  1  lcl|FitnessBrowser__MR1:200301  SO1121 glutamate 5-kinase (NCBI 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200301  SO1121 glutamate 5-kinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.0   3.0    4e-147    4e-147       1     363 []       9     371 ..       9     371 .. 1.00

  Alignments for each domain:
  == domain 1  score: 476.0 bits;  conditional E-value: 4e-147
                       TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgrL 79 
                                     +r+VvKlG+s+Lt++s++l++++++el++q+a+l++ G evv+ +SGa+aaG e+L +p  p ++a+kQ+laaVGQ++L
  lcl|FitnessBrowser__MR1:200301   9 RRVVVKLGTSVLTSGSKQLDKAHMVELARQMAALMRSGVEVVLCTSGAIAAGREHLQYPALPDTMANKQLLAAVGQSQL 87 
                                     59***************************************************************************** PP

                       TIGR01027  80 mklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalveA 158
                                     + ++ +lfs+ygl+v+Q+LLtradl++rerylNar+tl++ll+++++pi+NEND+va++eik+GDND+Lsa  a l +A
  lcl|FitnessBrowser__MR1:200301  88 ILAWAQLFSIYGLHVGQLLLTRADLHDRERYLNARDTLNALLANNIIPIINENDAVATNEIKVGDNDNLSARAALLCDA 166
                                     ******************************************************************************* PP

                       TIGR01027 159 dlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasgekpek 237
                                     dlL+lltd++gL+dadprtnp+Akli++ve+i+++l+ +ag+s s +GTGGm+tKleaa++A rag+ev+iasg++p+ 
  lcl|FitnessBrowser__MR1:200301 167 DLLILLTDQKGLFDADPRTNPNAKLISQVEKIDDSLRLLAGGSVSGLGTGGMSTKLEAADIARRAGIEVVIASGHHPDV 245
                                     ******************************************************************************* PP

                       TIGR01027 238 iadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaee 316
                                     i ++++++++gt f a ++ l++rkqwila+++a+G++++d+ga++a++ekg+sLl +g+++v+g+F+rg ++++++++
  lcl|FitnessBrowser__MR1:200301 246 IKKVVAKESIGTHFSAIENPLESRKQWILAGPAAQGSLVLDAGAVKAVTEKGRSLLSKGIIGVKGEFERGATLQLVDQN 324
                                     ******************************************************************************* PP

                       TIGR01027 317 gqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlvl 363
                                     g++i++g ++y  e+l  i+g++s+eie vLgy + + +vhr+++v+
  lcl|FitnessBrowser__MR1:200301 325 GKIIARGITRYCGEALGLIAGKHSDEIESVLGYDYGDAIVHRNDMVV 371
                                     ********************************************985 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.96
//
[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