Alignments for a candidate for hisG in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Methylocella silvestris BL2

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012589843.1 MSIL_RS04145 ATP phosphoribosyltransferase

Query= reanno::Caulo:CCNA_03626
         (320 letters)



>NCBI__GCF_000021745.1:WP_012589843.1
          Length = 325

 Score =  271 bits (694), Expect = 1e-77
 Identities = 156/322 (48%), Positives = 205/322 (63%), Gaps = 7/322 (2%)

Query: 1   MSTPMIFAIPSKGRLKDQVEAWLADCGFKLEMTGGARGYSAELSGLPGVSVRLLSAGDIA 60
           MS P + A+PSKGRL++   A+ A  G ++    GAR Y   L G+  V +  LSA DI 
Sbjct: 1   MSDPFVLAVPSKGRLQENAAAFFARAGLEIAQGRGARDYRGSLVGVKNVEIAFLSAADIV 60

Query: 61  AGLDSGDLHLGVTGEDLLRERGDDMDSRVMLLRALGFGRADLVVTAPKNWLDVDTMADVD 120
           A L SG +HLGVTGEDL+RE   D D +V LL  LGFG A++VV AP+ W+DV TMAD++
Sbjct: 61  AQLASGQVHLGVTGEDLVRESIADADDKVALLTPLGFGFANVVVAAPRAWIDVKTMADLE 120

Query: 121 EVGHAHLARTGRRLRVATKYVTQTRAFFARHGVADYRIVESSGATEGAPAAGAAELVVDI 180
           +V  ++ AR G+R+RVATKYV  TR FFA+  V+DYRIVESSGATEGAPAAG AEL+VDI
Sbjct: 121 DVAASYRARRGQRMRVATKYVNLTRRFFAKMHVSDYRIVESSGATEGAPAAGQAELIVDI 180

Query: 181 TTTGATLAANGLKILSDGVILKSQAQLTASLTAGWNGEQLDALRRLLSVVEAK--GRAGK 238
           TTTGATLAAN LKIL DG+IL+SQA L ASL+A W+G   +  R +LS + A+   R  +
Sbjct: 181 TTTGATLAANALKILDDGIILRSQANLVASLSADWSGPARENARAILSRIAAEELARTTR 240

Query: 239 LATLVWPAEQDRAAQDAVAAFIARGGSRRANGALLATADLFDAAAALAE----AGVEPVT 294
             + V P      A +A + F AR      +G +       +  AALA+     G + V 
Sbjct: 241 EVSTVLPCAPASLATEAQSLFSARLRFCAQDGRMSLNCPA-EKVAALADWLIGRGADHVG 299

Query: 295 VSRPDYVFESRSAVLDRFAEAL 316
           V+  DYVF + + + ++    L
Sbjct: 300 VTALDYVFSAENPLYEKLIAKL 321


Lambda     K      H
   0.318    0.133    0.375 

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: 245
Number of extensions: 8
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: 320
Length of database: 325
Length adjustment: 28
Effective length of query: 292
Effective length of database: 297
Effective search space:    86724
Effective search space used:    86724
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_012589843.1 MSIL_RS04145 (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.10200.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.6e-57  179.7   0.4    6.1e-57  178.5   0.3    1.6  2  lcl|NCBI__GCF_000021745.1:WP_012589843.1  MSIL_RS04145 ATP phosphoribosylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012589843.1  MSIL_RS04145 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.5   0.3   6.1e-57   6.1e-57       3     183 .]       7     209 ..       5     209 .. 0.93
   2 ?   -2.0   0.0      0.15      0.15      56      79 ..     291     314 ..     289     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 178.5 bits;  conditional E-value: 6.1e-57
                                 TIGR00070   3 iAlp.KGrleeetlkllekaglklskke.erkliasaed.eevevlllrakdiptyvekgaadlGitGk 68 
                                               +A+p KGrl+e++ +++++agl++ + + +r++  s    ++ve+ +l+a+di+ ++++g+++lG+tG+
  lcl|NCBI__GCF_000021745.1:WP_012589843.1   7 LAVPsKGRLQENAAAFFARAGLEIAQGRgARDYRGSLVGvKNVEIAFLSAADIVAQLASGQVHLGVTGE 75 
                                               8*************************9999****97766378*************************** PP

                                 TIGR00070  69 DlleEsead....vvelldlgfgkcklvlAvpees.dvesledlke...........gkriATkypnlt 121
                                               Dl++Es ad    v+ l+ lgfg +++v+A+p+++ dv++++dl++           ++r+ATky+nlt
  lcl|NCBI__GCF_000021745.1:WP_012589843.1  76 DLVRESIADaddkVALLTPLGFGFANVVVAAPRAWiDVKTMADLEDvaasyrarrgqRMRVATKYVNLT 144
                                               *****65555567999*************************************997555********** PP

                                 TIGR00070 122 reylekkg.vkveivkleGavElapllgladaIvDivetGttLrengLkiiee..ilessarlia 183
                                               r++++k++  +++iv+++Ga+E ap++g a++IvDi++tG+tL++n Lki+++  il+s+a+l+a
  lcl|NCBI__GCF_000021745.1:WP_012589843.1 145 RRFFAKMHvSDYRIVESSGATEGAPAAGQAELIVDITTTGATLAANALKILDDgiILRSQANLVA 209
                                               ********778****************************************9556********96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.15
                                 TIGR00070  56 vekgaadlGitGkDlleEseadvv 79 
                                               + +ga ++G+t  D++   e+ ++
  lcl|NCBI__GCF_000021745.1:WP_012589843.1 291 IGRGADHVGVTALDYVFSAENPLY 314
                                               5689999*******9988666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (325 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.40
//
[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