Alignments for a candidate for hisG in Desulfacinum infernum DSM 9756

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Desulfacinum infernum DSM 9756

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_084075750.1 BUB04_RS00270 ATP phosphoribosyltransferase

Query= reanno::Miya:8501229
         (293 letters)



>NCBI__GCF_900129305.1:WP_084075750.1
          Length = 290

 Score =  375 bits (964), Expect = e-109
 Identities = 187/287 (65%), Positives = 225/287 (78%)

Query: 7   LKIGIPKGSLEEATVNLFARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRYLEDGVL 66
           L +GIPKGSL+EAT+ LF +SGWKI   +RNYFPEINDPE+   +CR QE+ RY+E+G  
Sbjct: 4   LILGIPKGSLQEATIALFLKSGWKISLTNRNYFPEINDPEIQCSICRAQEMSRYVENGTF 63

Query: 67  DVGLTGKDWLLETGADVVTVSDLVYSKVSNRPARWVLAVAGDSPYVRPEDLAGCTIATEL 126
           DVGLTGKDW++E  +DV  V+DL+YSKVS RPARWVLAV  DSP    +DL G  IATEL
Sbjct: 64  DVGLTGKDWIMENDSDVHVVADLIYSKVSQRPARWVLAVPYDSPVQDLQDLQGKKIATEL 123

Query: 127 LGVTRRYFEDAGIPVKVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRIIAEVLLT 186
           +  TRRYF  AG+ VKV++SWGATEAKV+ GL DAIVEVTETG T++A+GLRI+ E++ +
Sbjct: 124 VNFTRRYFAQAGVDVKVEFSWGATEAKVIAGLCDAIVEVTETGATMRANGLRIVKELMQS 183

Query: 187 NTVLIAGKAAWADPWKRAKIEQIDLLLQGALRADSLVGLKMNVPAHNLDAVLDQLPSLNS 246
           NT LIA K AWADPWKR KIEQI LLLQ ALRA+ LVGLKMNVP   L+ V++ LPSL S
Sbjct: 184 NTQLIANKQAWADPWKREKIEQIALLLQAALRAEDLVGLKMNVPKGKLNDVIEILPSLTS 243

Query: 247 PTVAGLRDSTWYAVEIVVENDLVRDLIPRLRAAGAEGIIEYSLNKVI 293
           PT A L  S W +VE+VV   +VR+L+P+L   GAEGIIEYSLNKVI
Sbjct: 244 PTTAHLYQSDWVSVEVVVSKHMVRELVPQLIKRGAEGIIEYSLNKVI 290


Lambda     K      H
   0.318    0.136    0.401 

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: 340
Number of extensions: 14
Number of successful extensions: 1
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: 293
Length of database: 290
Length adjustment: 26
Effective length of query: 267
Effective length of database: 264
Effective search space:    70488
Effective search space used:    70488
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: 48 (23.1 bits)

Align candidate WP_084075750.1 BUB04_RS00270 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))

# 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/TIGR00070.hmm
# target sequence database:        /tmp/gapView.31648.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00070  [M=183]
Accession:   TIGR00070
Description: hisG: ATP phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-57  180.8   0.0    2.6e-57  179.8   0.0    1.5  2  lcl|NCBI__GCF_900129305.1:WP_084075750.1  BUB04_RS00270 ATP phosphoribosyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_084075750.1  BUB04_RS00270 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   2.6e-57   2.6e-57       2     183 .]       5     189 ..       4     189 .. 0.97
   2 ?   -2.3   0.0      0.18      0.18       1      12 [.     222     233 ..     222     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 2.6e-57
                                 TIGR00070   2 riAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDl 70 
                                                +++pKG+l+e t++l+ k+g+k+s ++ r+++ +++d+e+++ ++ra+++ +yve+g +d+G+tGkD+
  lcl|NCBI__GCF_900129305.1:WP_084075750.1   5 ILGIPKGSLQEATIALFLKSGWKISLTN-RNYFPEINDPEIQCSICRAQEMSRYVENGTFDVGLTGKDW 72 
                                               589*************************.**************************************** PP

                                 TIGR00070  71 leEseadvvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkvei 134
                                               ++E+++dv  ++dl ++k      ++vlAvp +s+v++l+dl+ gk+iAT+ +n tr+y+++ gv+v++
  lcl|NCBI__GCF_900129305.1:WP_084075750.1  73 IMENDSDVHVVADLIYSKVsqrpaRWVLAVPYDSPVQDLQDLQ-GKKIATELVNFTRRYFAQAGVDVKV 140
                                               **************8888767777*******************.9************************ PP

                                 TIGR00070 135 vkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                                 ++Ga+E+++++gl daIv ++etG+t+r+ngL+i++e+++s++ lia
  lcl|NCBI__GCF_900129305.1:WP_084075750.1 141 EFSWGATEAKVIAGLCDAIVEVTETGATMRANGLRIVKELMQSNTQLIA 189
                                               ***********************************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.18
                                 TIGR00070   1 lriAlpKGrlee 12 
                                               l++ +pKG+l +
  lcl|NCBI__GCF_900129305.1:WP_084075750.1 222 LKMNVPKGKLND 233
                                               688899999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (290 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: 00:00:00.00
# Mc/sec: 8.31
//
[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