Alignments for a candidate for proB in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Sulfurihydrogenibium subterraneum DSM 15120

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_028950520.1 Q385_RS0104490 glutamate 5-kinase

Query= BRENDA::Q6E235
         (370 letters)



>NCBI__GCF_000619805.1:WP_028950520.1
          Length = 367

 Score =  211 bits (536), Expect = 3e-59
 Identities = 146/364 (40%), Positives = 206/364 (56%), Gaps = 11/364 (3%)

Query: 2   KKQRIVVKIGSSSLTNSNGSIDEAKIKEHTEAISLLKENGHEVILITSGAVAAGFSALGY 61
           K +RIV+KIGS  L   N  ID   IK+    I    +   E I+++SGAV AG   L  
Sbjct: 9   KAKRIVIKIGSQILEKDN-DIDTDFIKDLANQIKNYPDK--EFIIVSSGAVLAGVKKLKL 65

Query: 62  PARPVTIKGKQAAAAVGQTLLMQQYMDHLKRYGLTPAQILLTRNDFSKRERYRNAYATVM 121
           P++P TI  KQA A+VGQ  LMQ Y        L   Q+LLT     +R+RY  A  T+ 
Sbjct: 66  PSKPKTITEKQAVASVGQAYLMQIYDKIFSEKDLIIGQMLLTIEGLQERKRYLYAKETLN 125

Query: 122 ELLERGVVPIINENDSTSVEELTFGDNDMLSALVSGLIHADQLMILTDINGLYDANPNEN 181
           +LLE  V+PIINEND+ +VEE+ FGDND LS+ VS L  AD L+I++   GLY  +P+ +
Sbjct: 126 KLLEYKVIPIINENDAIAVEEIVFGDNDYLSSHVSVLADADLLIIISTAGGLYTDDPS-S 184

Query: 182 PDAKRFDYLTDITPELLGYAGSAGSKVGTGGMKSKFLAAQTALSLGVKVFIGTGAGREKL 241
           P+A+    + D+    L YA S+ S  GTGGM+SK  AA+ A S  + V I        +
Sbjct: 185 PNAQLIKEVFDV-DYALNYAKSSKSTFGTGGMRSKLEAAKIATSHSIPVMI-VPKKSGII 242

Query: 242 KVILDGKGDGTYIGDKELSTVNNTRQWIMFHSPISGEIIIDGGAEQAMIHNGSSLLPAGV 301
            ++L+G+  GT+I   +   ++  + W+   S   G I++D GAE+A +  G SLLP+GV
Sbjct: 243 DMVLNGQEVGTFIYPSKKKKMSGKKSWLALLSHPKGRIVVDKGAEKA-LKEGKSLLPSGV 301

Query: 302 ADVCGSF-PKGAVVEVRGPGGIIGKGQTHYSSDEILEAKG---KRSDQLPGAKQVEVIHR 357
            +V G F PK  V  V     +IGKG  + S  ++ + KG   K + Q+ G    EVIHR
Sbjct: 302 KEVEGIFNPKDTVAIVNEENIVIGKGIINLSYKDLKKIKGLKTKEASQILGKDVEEVIHR 361

Query: 358 NDWV 361
           ++ V
Sbjct: 362 DNLV 365


Lambda     K      H
   0.314    0.134    0.377 

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: 361
Number of extensions: 22
Number of successful extensions: 7
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: 370
Length of database: 367
Length adjustment: 30
Effective length of query: 340
Effective length of database: 337
Effective search space:   114580
Effective search space used:   114580
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: 42 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_028950520.1 Q385_RS0104490 (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.17509.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-120  388.6   2.7   1.7e-120  388.4   2.7    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028950520.1  Q385_RS0104490 glutamate 5-kinas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028950520.1  Q385_RS0104490 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.4   2.7  1.7e-120  1.7e-120       1     363 []      11     366 ..      11     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 388.4 bits;  conditional E-value: 1.7e-120
                                 TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 
                                               kriV+K+Gs +L+++++ +++  +++l++q+++  +  +e +ivsSGav aG+++L lp++pk+++ekQ
  lcl|NCBI__GCF_000619805.1:WP_028950520.1  11 KRIVIKIGSQILEKDND-IDTDFIKDLANQIKNYPD--KEFIIVSSGAVLAGVKKLKLPSKPKTITEKQ 76 
                                               69**********99998.**************9876..69***************************** PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               a+a+VGQ++Lm+ y+k+fs+ +l ++Q+LLt + l++r+ryl a++tl++lle +v+pi+NEND++ave
  lcl|NCBI__GCF_000619805.1:WP_028950520.1  77 AVASVGQAYLMQIYDKIFSEKDLIIGQMLLTIEGLQERKRYLYAKETLNKLLEYKVIPIINENDAIAVE 145
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207
                                               ei fGDND Ls  v+ l +AdlL++++++ gLy++dp + p+A+li+ev +++ +l++ + ss s++GT
  lcl|NCBI__GCF_000619805.1:WP_028950520.1 146 EIVFGDNDYLSSHVSVLADADLLIIISTAGGLYTDDP-SSPNAQLIKEVFDVDYALNYAK-SSKSTFGT 212
                                               *************************************.9*************99998877.55688*** PP

                                 TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeak.kkklknrkqwilaaseakGki 275
                                               GGmr+Kleaa++A++  ++v+i+++++   i  +l++++vgt++ ++ kkk++ +k w++ +s++kG+i
  lcl|NCBI__GCF_000619805.1:WP_028950520.1 213 GGMRSKLEAAKIATSHSIPVMIVPKKS-GIIDMVLNGQEVGTFIYPSkKKKMSGKKSWLALLSHPKGRI 280
                                               ************************996.889999************94555****************** PP

                                 TIGR01027 276 ivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeie 344
                                               +vd+gae+al+e gksLlp+gv eveg F+  ++v i++ee   igkg  n s ++l+kikglk++e +
  lcl|NCBI__GCF_000619805.1:WP_028950520.1 281 VVDKGAEKALKE-GKSLLPSGVKEVEGIFNPKDTVAIVNEENIVIGKGIINLSYKDLKKIKGLKTKEAS 348
                                               ***********9.******************************************************** PP

                                 TIGR01027 345 dvLgyekkeevvhrdnlvl 363
                                               ++Lg    eev+hrdnlv+
  lcl|NCBI__GCF_000619805.1:WP_028950520.1 349 QILGKD-VEEVIHRDNLVI 366
                                               ***876.789******985 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: 9.49
//
[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