Alignments for a candidate for hisA in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisA in Methanococcus aeolicus Nankai-3

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_011973909.1 MAEO_RS06090 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase

Query= reanno::Cola:Echvi_2515
         (239 letters)



>NCBI__GCF_000017185.1:WP_011973909.1
          Length = 241

 Score =  161 bits (407), Expect = 1e-44
 Identities = 94/234 (40%), Positives = 139/234 (59%), Gaps = 2/234 (0%)

Query: 1   MEIIPAIDIIGGKCVRLTQGDYGQKKEYADNPLEVAKKFEGAGIKRLHLVDLDGAKAKTI 60
           M +IPA+DI   KCV+L QG+  +K    DNPLEVA+K+   G + +HLVDLD A   T 
Sbjct: 1   MIVIPAVDIKNKKCVQLIQGNPDKKHIELDNPLEVAEKWIKCGAEMIHLVDLDSAIYGTD 60

Query: 61  VNRAVLENITSHTSLKVDFGGGVQSDETIQMAFDAGASQVTGGSIAVKNPALFEGWLEKH 120
            N+  ++ I     + V+ GGGV++ E      D GA +V  G+ AVKNP +    LEK 
Sbjct: 61  TNKETIKKIIESVPVPVEVGGGVRTVEDALNLIDLGAERVILGTSAVKNPEIITELLEKG 120

Query: 121 -GSEKIILGADAKNRKIAISGWEETTEADVVDFIKDYHAKGARYVICTDVAKDGLLQGPS 179
             SEKI++  DAK+ K+ I GW E TE   ++  K    KGA  ++ T+V  +GLL G  
Sbjct: 121 INSEKIMVALDAKDGKVVIKGWMEKTEYTPIEIGKILEEKGAGSILFTNVDVEGLLDGID 180

Query: 180 VDLYREIIQEIPGIRLIASGGVAEVRDLEVLEKIGVFGTIVGKAFYEGRVSLEE 233
           ++  ++++ E+  I +IASGG+    DL  L++IGV G +VG A Y+  + L++
Sbjct: 181 IEPVKKLVDEL-NIPIIASGGITTYDDLLKLKEIGVDGVVVGSAIYKEMMDLKK 233


Lambda     K      H
   0.317    0.138    0.391 

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: 190
Number of extensions: 13
Number of successful extensions: 3
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: 241
Length adjustment: 23
Effective length of query: 216
Effective length of database: 218
Effective search space:    47088
Effective search space used:    47088
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 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate WP_011973909.1 MAEO_RS06090 (1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase)
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.20510.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.8e-84  267.9   5.9    4.3e-84  267.7   5.9    1.0  1  lcl|NCBI__GCF_000017185.1:WP_011973909.1  MAEO_RS06090 1-(5-phosphoribosyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_011973909.1  MAEO_RS06090 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.7   5.9   4.3e-84   4.3e-84       1     230 [.       3     233 ..       3     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 4.3e-84
                                 TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 
                                               +iPa+D+k+ k+v+l+qG++dkk+++ d+ple+a+k+ + gae++H+VDLd A+ g  +n+e+ikki+e
  lcl|NCBI__GCF_000017185.1:WP_011973909.1   3 VIPAVDIKNKKCVQLIQGNPDKKHIELDNPLEVAEKWIKCGAEMIHLVDLDSAIYGTDTNKETIKKIIE 71 
                                               89******************************************************************* PP

                                 TIGR00007  70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellke.lgsekivvslDakegevavk 137
                                               ++ v+v+vGGG+R++e++ +l++lg+ervi+gt+av+npe+++ell++ ++seki+v+lDak+g+v++k
  lcl|NCBI__GCF_000017185.1:WP_011973909.1  72 SVPVPVEVGGGVRTVEDALNLIDLGAERVILGTSAVKNPEIITELLEKgINSEKIMVALDAKDGKVVIK 140
                                               *********************************************98757889**************** PP

                                 TIGR00007 138 GWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvka 206
                                               GW ek+e++++e+ k lee g+ +i++T+++++G l G+++e +k+lv+e ++++iasGG+++ +d+ +
  lcl|NCBI__GCF_000017185.1:WP_011973909.1 141 GWMEKTEYTPIEIGKILEEKGAGSILFTNVDVEGLLDGIDIEPVKKLVDELNIPIIASGGITTYDDLLK 209
                                               ********************************************************************* PP

                                 TIGR00007 207 lkklgvkgvivGkAlyegklklke 230
                                               lk++gv+gv+vG+A+y++ ++lk+
  lcl|NCBI__GCF_000017185.1:WP_011973909.1 210 LKEIGVDGVVVGSAIYKEMMDLKK 233
                                               ********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (241 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: 00:00:00.00
# Mc/sec: 7.57
//
[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