Aligments for a candidate for proB in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Aligments for a candidate for proB in Shewanella sp. ANA-3

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 7023724 Shewana3_0954 gamma-glutamyl kinase (RefSeq)

Query= BRENDA::P0A7B5
         (367 letters)



>lcl|FitnessBrowser__ANA3:7023724 Shewana3_0954 gamma-glutamyl
           kinase (RefSeq)
          Length = 372

 Score =  446 bits (1146), Expect = e-130
 Identities = 230/360 (63%), Positives = 282/360 (78%), Gaps = 1/360 (0%)

Query: 7   LVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELP 66
           +VVKLGTSVLT GS++L++AH+VEL RQ A L  +G  +V+ TSGAIAAGREHL YPELP
Sbjct: 11  VVVKLGTSVLTSGSKQLDKAHMVELARQMAALMRSGVEVVLCTSGAIAAGREHLQYPELP 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
              SVGT F A   PLE+RK+WI   P A G + +D GA  A+ E+G SLL KGI  V G
Sbjct: 251 GKESVGTHFSAIENPLESRKQWILAGPAAQGSLVLDAGAVKAVTEKGRSLLSKGIIGVKG 310

Query: 306 NFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
            F RG  +++ + +G+ IA G++RY  +AL  IAG HS EI+++LGY+YG   VHR+DM+
Sbjct: 311 EFERGATLQLVDQKGKIIARGITRYCGEALGLIAGKHSDEIESVLGYDYGDAIVHRNDMV 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: 409
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 7023724 Shewana3_0954 (gamma-glutamyl kinase (RefSeq))
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.10088.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-147  476.7   2.7   2.8e-147  476.6   2.7    1.0  1  lcl|FitnessBrowser__ANA3:7023724  Shewana3_0954 gamma-glutamyl kin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023724  Shewana3_0954 gamma-glutamyl kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.6   2.7  2.8e-147  2.8e-147       1     363 []       9     371 ..       9     371 .. 1.00

  Alignments for each domain:
  == domain 1  score: 476.6 bits;  conditional E-value: 2.8e-147
                         TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQg 77 
                                       +r+VvKlG+s+Lt++s++l++++++el++q+a+l++ G evv+ +SGa+aaG e+L +pe p ++a+kQ+laaVGQ+
  lcl|FitnessBrowser__ANA3:7023724   9 RRVVVKLGTSVLTSGSKQLDKAHMVELARQMAALMRSGVEVVLCTSGAIAAGREHLQYPELPDTMANKQLLAAVGQS 85 
                                       59*************************************************************************** PP

                         TIGR01027  78 rLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaa 154
                                       +L+ ++ +lfs+ygl+v+Q+LLtradl++rerylNar+tl++ll+++++pi+NEND+va++eik+GDND+Lsa  a 
  lcl|FitnessBrowser__ANA3:7023724  86 QLILAWAQLFSIYGLHVGQLLLTRADLHDRERYLNARDTLNALLANNIIPIINENDAVATNEIKVGDNDNLSARAAL 162
                                       ***************************************************************************** PP

                         TIGR01027 155 lveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviias 231
                                       l +AdlL+lltd++gL+dadprtnp+Akli++ve+i+++l+ +ag+s s +GTGGm+tKleaa++A rag+ev+ias
  lcl|FitnessBrowser__ANA3:7023724 163 LCDADLLILLTDQKGLFDADPRTNPNAKLISQVEKIDDSLRLLAGGSVSGLGTGGMSTKLEAADIARRAGIEVVIAS 239
                                       ***************************************************************************** PP

                         TIGR01027 232 gekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrge 308
                                       g++p+ i +++ +++vgt f a ++ l++rkqwila+++a+G++++d+ga++a++ekg+sLl +g+++v+g+F+rg 
  lcl|FitnessBrowser__ANA3:7023724 240 GHHPDVIKKVVGKESVGTHFSAIENPLESRKQWILAGPAAQGSLVLDAGAVKAVTEKGRSLLSKGIIGVKGEFERGA 316
                                       ***************************************************************************** PP

                         TIGR01027 309 vveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlvl 363
                                       ++++++++g++i++g ++y  e+l  i+g++s+eie vLgy + + +vhr+++v+
  lcl|FitnessBrowser__ANA3:7023724 317 TLQLVDQKGKIIARGITRYCGEALGLIAGKHSDEIESVLGYDYGDAIVHRNDMVV 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.08
//
[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