Alignments for a candidate for proB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Synechococcus elongatus PCC 7942

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Synpcc7942_2197 Synpcc7942_2197 gamma-glutamyl kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__SynE:Synpcc7942_2197
          Length = 367

 Score =  284 bits (726), Expect = 3e-81
 Identities = 156/364 (42%), Positives = 222/364 (60%), Gaps = 2/364 (0%)

Query: 4   SQTLVVKLGTSVLTGGSRR-LNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGY 62
           S+TLVVK+GTS LT      L  + I  LV    QL   G+ +V+V+SGA+  G   LG 
Sbjct: 2   SETLVVKIGTSSLTNPHHPGLALSTIAGLVEVICQLRRQGYNVVLVSSGAVGVGCTRLGL 61

Query: 63  PELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLR 122
            + P+ IA +Q +AAVGQ RL++ ++ LF+  G  + Q+LLTR D+  R+R++NA  T +
Sbjct: 62  RDRPSRIAQRQAIAAVGQGRLMRTYDDLFTTLGQPIAQVLLTRGDLAQRQRYINAYQTFQ 121

Query: 123 ALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSN 182
            L +  +VP++NEND VA  E+K GDND LSAL A L  A  L LLTD   LYTADPR +
Sbjct: 122 ELFELGVVPIVNENDTVAVEELKFGDNDTLSALVASLVEAQWLFLLTDVDRLYTADPRQD 181

Query: 183 PQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVI 242
           P A+ I  V+ + +     AG   S  GTGGM+TKL AA +A +A + T+I  G  P  +
Sbjct: 182 PNAKPITIVHDLSELESIQAGGQGSRWGTGGMATKLTAAKIATQASVRTVITQGRSPENL 241

Query: 243 GDVMEGISVGTLFHAQATPLENRKRWI-FGAPPAGEITVDEGATAAILERGSSLLPKGIK 301
             ++ G ++GT F  Q   +  RKRWI  G  P G++ +D GA  AI   G SLL  GI+
Sbjct: 242 LKILAGEAIGTWFEPQPETVNARKRWIAHGLVPTGKLLLDAGAVQAIQAGGKSLLAAGIQ 301

Query: 302 SVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHR 361
           ++ G+F   + +++C+L G +IA G+  Y+S  L++I G  S +I  ILGYE     VHR
Sbjct: 302 AIEGDFEAQDAVQLCDLNGTEIARGLVNYDSHELQQIRGCQSDQIVQILGYEGAETIVHR 361

Query: 362 DDMI 365
           D+++
Sbjct: 362 DNLV 365


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: 323
Number of extensions: 12
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: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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 Synpcc7942_2197 Synpcc7942_2197 (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.23509.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-148  481.0   0.2   1.4e-148  480.8   0.2    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2197  Synpcc7942_2197 gamma-glutamyl k


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2197  Synpcc7942_2197 gamma-glutamyl kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.8   0.2  1.4e-148  1.4e-148       2     362 ..       4     365 ..       3     366 .. 0.99

  Alignments for each domain:
  == domain 1  score: 480.8 bits;  conditional E-value: 1.4e-148
                                 TIGR01027   2 riVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 
                                               ++VvK+G+ssLt++++  l++s++a lve +++l+++G +vv+vsSGav +G+++Lgl +rp ++a++Q
  lcl|FitnessBrowser__SynE:Synpcc7942_2197   4 TLVVKIGTSSLTNPHHPgLALSTIAGLVEVICQLRRQGYNVVLVSSGAVGVGCTRLGLRDRPSRIAQRQ 72 
                                               89************9988*************************************************** PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               a+aaVGQgrLm++y++lf + g+ +aQ+LLtr dl++r+ry Na++t++el+elgvvpivNENDtvave
  lcl|FitnessBrowser__SynE:Synpcc7942_2197  73 AIAAVGQGRLMRTYDDLFTTLGQPIAQVLLTRGDLAQRQRYINAYQTFQELFELGVVPIVNENDTVAVE 141
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207
                                               e+kfGDNDtLsalva+lveA++L+lltdvd+Ly+adpr++p+Ak+i  v++++e     ag+ gs++GT
  lcl|FitnessBrowser__SynE:Synpcc7942_2197 142 ELKFGDNDTLSALVASLVEAQWLFLLTDVDRLYTADPRQDPNAKPITIVHDLSELESIQAGGQGSRWGT 210
                                               ********************************************************************* PP

                                 TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276
                                               GGm+tKl+aa++A++a v+++i++g++pe+++++l+++a+gt fe++ +++++rk+wi++++ ++Gk++
  lcl|FitnessBrowser__SynE:Synpcc7942_2197 211 GGMATKLTAAKIATQASVRTVITQGRSPENLLKILAGEAIGTWFEPQPETVNARKRWIAHGLVPTGKLL 279
                                               ********************************************************************* PP

                                 TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeied 345
                                               +d+ga++a+++ gksLl+ag+ ++eg+F++ ++v++++ +g+ei++glvny+s+el++i g +s++i +
  lcl|FitnessBrowser__SynE:Synpcc7942_2197 280 LDAGAVQAIQAGGKSLLAAGIQAIEGDFEAQDAVQLCDLNGTEIARGLVNYDSHELQQIRGCQSDQIVQ 348
                                               ********************************************************************* PP

                                 TIGR01027 346 vLgyekkeevvhrdnlv 362
                                               +Lgye  e++vhrdnlv
  lcl|FitnessBrowser__SynE:Synpcc7942_2197 349 ILGYEGAETIVHRDNLV 365
                                               ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (367 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: 7.05
//
[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