Alignments for a candidate for proB in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Denitrovibrio acetiphilus DSM 12809

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_013011162.1 DACET_RS09500 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_000025725.1:WP_013011162.1
          Length = 380

 Score =  282 bits (721), Expect = 1e-80
 Identities = 159/366 (43%), Positives = 227/366 (62%), Gaps = 5/366 (1%)

Query: 5   QTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPE 64
           +TLVVK+G+++LT   R +N   +  LVR           IV+V+SGA+ AG + LG+ E
Sbjct: 8   ETLVVKVGSNILTHHERGVNLEFLSGLVRILCNFKKNIPNIVVVSSGAVGAGFKLLGFSE 67

Query: 65  LPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRAL 124
            P  I  KQ  AAVGQ+RLI  +++ F  YG+   Q+L+T+ D+ +R R+LNAR TLR L
Sbjct: 68  RPQNITDKQACAAVGQARLIWEYDREFEKYGVTSAQILITKDDLSNRRRYLNARYTLRRL 127

Query: 125 LDNNIVPVINENDAVATAEIK----VGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           L+  +VPVINEND+V   E++      DNDNLSAL + L GAD LL+L+D  GL+  DP 
Sbjct: 128 LELGVVPVINENDSVVIEELRQIENFTDNDNLSALVSGLIGADMLLILSDVDGLFDKDPF 187

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
            N  A+ I++V  I++ L  +AGDSVSG+GTGGM +KL+AA  A  AG    I  G    
Sbjct: 188 KNKDAKRIEEVKYINEELLNVAGDSVSGVGTGGMKSKLEAAGKALDAGCHVGIINGMNLF 247

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWI-FGAPPAGEITVDEGATAAILERGSSLLPKG 299
            +   + G  VGT F+    PL  RK WI + A  +GE+ VD GA  A++ + +SLLP G
Sbjct: 248 NVEAFLNGEDVGTFFNHIEDPLTRRKHWIAYAAGASGELHVDNGAVNALVNKKTSLLPSG 307

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +  VTG+F  G+V+ +   +G+++A G  RY S+    I G  S +I +ILGY++    +
Sbjct: 308 VTKVTGHFGMGDVVAVIGPDGKEVARGKVRYASEDADLIKGKKSSDISSILGYKFTDEII 367

Query: 360 HRDDMI 365
           HRDD++
Sbjct: 368 HRDDLV 373


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: 373
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: 380
Length adjustment: 30
Effective length of query: 337
Effective length of database: 350
Effective search space:   117950
Effective search space used:   117950
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_013011162.1 DACET_RS09500 (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.27608.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-133  430.8   0.2   2.5e-133  430.6   0.2    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013011162.1  DACET_RS09500 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013011162.1  DACET_RS09500 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.6   0.2  2.5e-133  2.5e-133       2     362 ..       9     373 ..       8     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 430.6 bits;  conditional E-value: 2.5e-133
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQa 70 
                                               ++VvK+Gs++Lt++++ ++++ l+ lv+ +++ kk+  ++v+vsSGav aG++ Lg++erp+++++kQa
  lcl|NCBI__GCF_000025725.1:WP_013011162.1   9 TLVVKVGSNILTHHERGVNLEFLSGLVRILCNFKKNIPNIVVVSSGAVGAGFKLLGFSERPQNITDKQA 77 
                                               89******************************************************************* PP

                                 TIGR01027  71 laaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvavee 139
                                                aaVGQ+rL+ +y++ f++yg ++aQiL+t++dls+r+rylNar tl++llelgvvp++NEND+v +ee
  lcl|NCBI__GCF_000025725.1:WP_013011162.1  78 CAAVGQARLIWEYDREFEKYGVTSAQILITKDDLSNRRRYLNARYTLRRLLELGVVPVINENDSVVIEE 146
                                               ********************************************************************* PP

                                 TIGR01027 140 i....kfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgss 204
                                               +    +f DND+Lsalv+ l++Ad+L++l+dvdgL+d+dp +n dAk+ieev+ i+eel +vag+s s 
  lcl|NCBI__GCF_000025725.1:WP_013011162.1 147 LrqieNFTDNDNLSALVSGLIGADMLLILSDVDGLFDKDPFKNKDAKRIEEVKYINEELLNVAGDSVSG 215
                                               955555*************************************************************** PP

                                 TIGR01027 205 vGTGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakG 273
                                               vGTGGm++Kleaa  A +ag +v i++g +  ++ ++l+++ vgt+f+  +  l  rk+wi++a+ a+G
  lcl|NCBI__GCF_000025725.1:WP_013011162.1 216 VGTGGMKSKLEAAGKALDAGCHVGIINGMNLFNVEAFLNGEDVGTFFNHIEDPLTRRKHWIAYAAGASG 284
                                               ********************************************************************* PP

                                 TIGR01027 274 kiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglksee 342
                                               ++ vd+ga++al++k++sLlp+gv++v+g+F  g+vv +  ++g+e+++g+v+y se+   ikg+ks++
  lcl|NCBI__GCF_000025725.1:WP_013011162.1 285 ELHVDNGAVNALVNKKTSLLPSGVTKVTGHFGMGDVVAVIGPDGKEVARGKVRYASEDADLIKGKKSSD 353
                                               ********************************************************************* PP

                                 TIGR01027 343 iedvLgyekkeevvhrdnlv 362
                                               i+ +Lgy+ ++e++hrd+lv
  lcl|NCBI__GCF_000025725.1:WP_013011162.1 354 ISSILGYKFTDEIIHRDDLV 373
                                               ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (380 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: 9.44
//
[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