Alignments for a candidate for proB in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Halomonas desiderata SP1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_086508023.1 BZY95_RS00405 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_002151265.1:WP_086508023.1
          Length = 378

 Score =  303 bits (775), Expect = 7e-87
 Identities = 163/363 (44%), Positives = 235/363 (64%), Gaps = 2/363 (0%)

Query: 4   SQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYP 63
           ++ +VVK+G+++LT   R L+ A I   V Q A LH  G  +V+V+SGA+AAG   LG+ 
Sbjct: 15  ARRVVVKIGSALLTNDGRGLDEAAIGGWVDQIAALHRQGLEVVLVSSGAVAAGMVRLGWQ 74

Query: 64  ELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRA 123
             P+ +   Q  AAVGQ+ L Q +E  F+ +G+   Q+LLT  D+ +R+R+LNAR  LR 
Sbjct: 75  ARPSAVHELQAAAAVGQNGLTQCYEHHFARHGLLTAQVLLTHDDLSNRKRYLNARSALRT 134

Query: 124 LLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNP 183
           L+D  ++PVINEND V T EI+ GDND L AL A L  A+ L++LTDQ+GL+ ADPR NP
Sbjct: 135 LVDLRVIPVINENDTVVTDEIRFGDNDTLGALVANLLEAEALVILTDQEGLFDADPRHNP 194

Query: 184 QAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIG 243
           +A LI +    D AL A+AG     LG GGM+TK+QAA +A R+G  T+IA+G +P V+ 
Sbjct: 195 EASLISEGRADDPALAAMAGGG-GALGRGGMTTKVQAARLAARSGAVTVIASGRQPEVLT 253

Query: 244 DVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKGIKS 302
            + EG  +GTL   +  P+  RKRW+ G     G +T+D GA   +   GSSLL  G+K+
Sbjct: 254 RLAEGEPLGTLLRPEEAPMAARKRWLAGQLQVRGSLTLDAGAVKVLRGSGSSLLAVGVKA 313

Query: 303 VTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRD 362
           ++G+F RG+++   + +G+ IA G+  Y +D  RRI G  S +I+AILGY   P  +HRD
Sbjct: 314 LSGDFVRGDMVLCVDEQGQRIAKGLVNYGADEARRILGQPSHQIEAILGYMEAPELIHRD 373

Query: 363 DMI 365
           +++
Sbjct: 374 NLV 376


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: 382
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: 378
Length adjustment: 30
Effective length of query: 337
Effective length of database: 348
Effective search space:   117276
Effective search space used:   117276
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 WP_086508023.1 BZY95_RS00405 (glutamate 5-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.27315.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-131  423.2   0.2   5.4e-131  423.0   0.2    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508023.1  BZY95_RS00405 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508023.1  BZY95_RS00405 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.0   0.2  5.4e-131  5.4e-131       1     362 [.      16     376 ..      16     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: 423.0 bits;  conditional E-value: 5.4e-131
                                 TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 
                                               +r+VvK+Gs++Lt++ + l+++ +   v q+a+l+++G evv+vsSGavaaG+ +Lg + rp  ++e Q
  lcl|NCBI__GCF_002151265.1:WP_086508023.1  16 RRVVVKIGSALLTNDGRGLDEAAIGGWVDQIAALHRQGLEVVLVSSGAVAAGMVRLGWQARPSAVHELQ 84 
                                               59******************************************************************* PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               a+aaVGQ  L + ye+ f+++gl +aQ+LLt++dls+r+rylNar++l++l++l+v+p++NENDtv ++
  lcl|NCBI__GCF_002151265.1:WP_086508023.1  85 AAAAVGQNGLTQCYEHHFARHGLLTAQVLLTHDDLSNRKRYLNARSALRTLVDLRVIPVINENDTVVTD 153
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207
                                               ei+fGDNDtL alva+l+eA++Lv+ltd++gL+dadpr+np+A li+e ++ + +l a+ag++  ++G 
  lcl|NCBI__GCF_002151265.1:WP_086508023.1 154 EIRFGDNDTLGALVANLLEAEALVILTDQEGLFDADPRHNPEASLISEGRADDPALAAMAGGG-GALGR 221
                                               ************************************************************996.56*** PP

                                 TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276
                                               GGm+tK++aa+lA+r+g  ++iasg++pe +++l+e++++gtl+ ++++ + +rk+w++ +++ +G+++
  lcl|NCBI__GCF_002151265.1:WP_086508023.1 222 GGMTTKVQAARLAARSGAVTVIASGRQPEVLTRLAEGEPLGTLLRPEEAPMAARKRWLAGQLQVRGSLT 290
                                               ********************************************************************* PP

                                 TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeied 345
                                               +d+ga++ l+  g+sLl++gv +++g+F rg++v +++e+gq i+kglvny ++e ++i g++s++ie+
  lcl|NCBI__GCF_002151265.1:WP_086508023.1 291 LDAGAVKVLRGSGSSLLAVGVKALSGDFVRGDMVLCVDEQGQRIAKGLVNYGADEARRILGQPSHQIEA 359
                                               ********************************************************************* PP

                                 TIGR01027 346 vLgyekkeevvhrdnlv 362
                                               +Lgy +  e +hrdnlv
  lcl|NCBI__GCF_002151265.1:WP_086508023.1 360 ILGYMEAPELIHRDNLV 376
                                               ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (378 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.59
//
[ok]

This GapMind analysis is from Apr 10 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