GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Bacteroides thetaiotaomicron VPI-5482

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 350907 BT1379 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (NCBI ptt file)

Query= reanno::Btheta:350907
         (239 letters)



>FitnessBrowser__Btheta:350907
          Length = 239

 Score =  482 bits (1240), Expect = e-141
 Identities = 239/239 (100%), Positives = 239/239 (100%)

Query: 1   MIEIIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHH 60
           MIEIIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHH
Sbjct: 1   MIEIIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHH 60

Query: 61  VVNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEV 120
           VVNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEV
Sbjct: 61  VVNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEV 120

Query: 121 YGSEKIILGADVKEHKIAVNGWKDESACELFPFLEDYINKGIQKVICTDISCDGMLKGPS 180
           YGSEKIILGADVKEHKIAVNGWKDESACELFPFLEDYINKGIQKVICTDISCDGMLKGPS
Sbjct: 121 YGSEKIILGADVKEHKIAVNGWKDESACELFPFLEDYINKGIQKVICTDISCDGMLKGPS 180

Query: 181 IDLYKEMLEKFPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHITLKDLRIFL 239
           IDLYKEMLEKFPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHITLKDLRIFL
Sbjct: 181 IDLYKEMLEKFPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHITLKDLRIFL 239


Lambda     K      H
   0.320    0.140    0.413 

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: 333
Number of extensions: 5
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: 239
Length of database: 239
Length adjustment: 23
Effective length of query: 216
Effective length of database: 216
Effective search space:    46656
Effective search space used:    46656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate 350907 BT1379 (phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (NCBI ptt file))
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))

# 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/TIGR00007.hmm
# target sequence database:        /tmp/gapView.11928.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00007  [M=231]
Accession:   TIGR00007
Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    3.2e-79  251.8   0.1    3.6e-79  251.6   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350907  BT1379 phosphoribosylformimino-5


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350907  BT1379 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.6   0.1   3.6e-79   3.6e-79       1     230 [.       4     234 ..       4     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.6 bits;  conditional E-value: 3.6e-79
                          TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvq 76 
                                        iiPaiD+++Gk+vrl qGd+d+k+vy+++p+e+ak+fe++g+++lHvVDLdgA +++ +n +v+++i++++++ v+
  lcl|FitnessBrowser__Btheta:350907   4 IIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHHVVNHRVLEQIATRTSLIVD 79 
                                        8*************************************************************************** PP

                          TIGR00007  77 vGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvelak 152
                                         GGG++s e+++ ++e g++ v  g++av++pel+ ++l+ +gseki+++ D+ke+++av+GWk++s ++l+ +++
  lcl|FitnessBrowser__Btheta:350907  80 FGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEVYGSEKIILGADVKEHKIAVNGWKDESACELFPFLE 155
                                        **************************************************************************** PP

                          TIGR00007 153 kleelgleeiilTdiekdGtlsGvnveltkelvke.aeveviasGGvssiedvkalkklgvkgvivGkAlyegklk 227
                                         + + g++++i+Tdi+ dG+l+G+ ++l+ke++++  +  ++asGGvs+++d++al+++gv gvi GkAlyeg+++
  lcl|FitnessBrowser__Btheta:350907 156 DYINKGIQKVICTDISCDGMLKGPSIDLYKEMLEKfPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHIT 231
                                        **************************************************************************** PP

                          TIGR00007 228 lke 230
                                        lk+
  lcl|FitnessBrowser__Btheta:350907 232 LKD 234
                                        986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (239 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: 6.85
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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