Alignments for a candidate for proB in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_018232926.1 THITHI_RS0118025 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_000378965.1:WP_018232926.1
          Length = 375

 Score =  290 bits (741), Expect = 6e-83
 Identities = 152/359 (42%), Positives = 219/359 (61%), Gaps = 1/359 (0%)

Query: 8   VVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPA 67
           V+K+G+++LT   R L+   +     Q A+L   G  +V+V+SGA+A G   LG+   P 
Sbjct: 15  VIKIGSALLTNEGRGLDHDSLAAWAEQIARLRGTGREVVLVSSGAVAEGMRRLGWTVRPH 74

Query: 68  TIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDN 127
            +   Q  AAVGQ  L+Q +E +F  +G+   Q+LLT  D+ DR R+LNAR TLR LL  
Sbjct: 75  ALHELQAAAAVGQMGLVQAYESIFQRHGLRAAQVLLTHDDLSDRRRYLNARSTLRTLLGL 134

Query: 128 NIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAEL 187
            ++PV+NEND VAT EI+ GDND L+AL   L  A  L++LTDQ+GL+  DPR++  A L
Sbjct: 135 GVIPVVNENDTVATDEIRFGDNDTLAALVGNLTEAQVLVILTDQQGLFDRDPRTHQDATL 194

Query: 188 IKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVME 247
           I +    D  L  +A      LG GGM+TKLQAA  A R+G  T+IA+G +P V+  + +
Sbjct: 195 ISEGMAADPELLKLAAPGFGHLGRGGMTTKLQAAARAARSGTYTLIASGREPRVLERIAD 254

Query: 248 GISVGTLFHAQATPLENRKRWIFGAPPA-GEITVDEGATAAILERGSSLLPKGIKSVTGN 306
           G  +GTL      P+  RK+WI G   + GE+ +D GA   + E G SLLP G+  V G 
Sbjct: 255 GEPLGTLLCPDREPIAARKQWIAGQMVSKGELLLDAGAARVVRESGRSLLPVGVTHVKGT 314

Query: 307 FSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
           F+RG+V+   + +GR +A G+  Y+++  RRI  H + EI+ ILGY   P  +HRD+++
Sbjct: 315 FTRGDVVTCLDPDGRPVARGLVNYSAEESRRIMRHRADEIEGILGYVDEPELIHRDNLV 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: 354
Number of extensions: 17
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: 375
Length adjustment: 30
Effective length of query: 337
Effective length of database: 345
Effective search space:   116265
Effective search space used:   116265
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 WP_018232926.1 THITHI_RS0118025 (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.1423320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-131  424.2   0.0   2.6e-131  424.0   0.0    1.0  1  NCBI__GCF_000378965.1:WP_018232926.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018232926.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.0   0.0  2.6e-131  2.6e-131       2     362 ..      13     373 ..      12     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.0 bits;  conditional E-value: 2.6e-131
                             TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaV 74 
                                           r V+K+Gs++Lt+e + l++  la+ +eq+a+l+ +G+evv+vsSGava G+++Lg + rp+ l+e Qa+aaV
  NCBI__GCF_000378965.1:WP_018232926.1  13 RWVIKIGSALLTNEGRGLDHDSLAAWAEQIARLRGTGREVVLVSSGAVAEGMRRLGWTVRPHALHELQAAAAV 85 
                                           67*********************************************************************** PP

                             TIGR01027  75 GQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDt 147
                                           GQ  L+++ye++f+++gl+ aQ+LLt++dls+r+rylNar+tl++ll lgv+p+vNENDtva++ei+fGDNDt
  NCBI__GCF_000378965.1:WP_018232926.1  86 GQMGLVQAYESIFQRHGLRAAQVLLTHDDLSDRRRYLNARSTLRTLLGLGVIPVVNENDTVATDEIRFGDNDT 158
                                           ************************************************************************* PP

                             TIGR01027 148 LsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelA 220
                                           L+alv +l eA++Lv+ltd++gL+d+dprt+ dA+li+e  +++ el ++a+ +  ++G GGm+tKl+aa  A
  NCBI__GCF_000378965.1:WP_018232926.1 159 LAALVGNLTEAQVLVILTDQQGLFDRDPRTHQDATLISEGMAADPELLKLAAPGFGHLGRGGMTTKLQAAARA 231
                                           *****************************************************9889**************** PP

                             TIGR01027 221 sragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLl 293
                                           +r+g  ++iasg++p  + ++++++++gtl+ + ++ + +rkqwi+ ++ +kG++++d+ga++ ++e g+sLl
  NCBI__GCF_000378965.1:WP_018232926.1 232 ARSGTYTLIASGREPRVLERIADGEPLGTLLCPDREPIAARKQWIAGQMVSKGELLLDAGAARVVRESGRSLL 304
                                           ************************************************************************* PP

                             TIGR01027 294 pagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                           p+gv++v+g+F+rg+vv++l+++g+ +++glvnys+ee ++i++++ +eie +Lgy ++ e +hrdnlv
  NCBI__GCF_000378965.1:WP_018232926.1 305 PVGVTHVKGTFTRGDVVTCLDPDGRPVARGLVNYSAEESRRIMRHRADEIEGILGYVDEPELIHRDNLV 373
                                           *******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (375 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: 10.02
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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