Alignments for a candidate for hisA in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisA in Halorhodospira halophila SL1

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_011813891.1 HHAL_RS05570 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= reanno::psRCH2:GFF155
         (247 letters)



>NCBI__GCF_000015585.1:WP_011813891.1
          Length = 246

 Score =  303 bits (777), Expect = 2e-87
 Identities = 148/236 (62%), Positives = 183/236 (77%), Gaps = 1/236 (0%)

Query: 1   MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60
           M++IPAIDLK+G CVRLRQG MDD T+F  DPVA+A +WVEAG  RLHLVDL+GA  G+P
Sbjct: 1   MIVIPAIDLKNGHCVRLRQGRMDDETIFDADPVAVAGRWVEAGAERLHLVDLDGAVRGEP 60

Query: 61  VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120
            + + + AIA+ YPD P+QIGGGIR+ ET   Y+ AGV YVI+GT+AV+EP FV E CR 
Sbjct: 61  AHEQTIHAIARAYPDTPLQIGGGIRSRETALRYLEAGVGYVIVGTRAVREPAFVEELCRE 120

Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180
            PG+V VGLDA+ G+VATDGW + S V AVDLARRFE  GV+A+++TDI +DGMMQGCNV
Sbjct: 121 IPGRVCVGLDARGGYVATDGWEQTSEVAAVDLARRFEDAGVAALIFTDIGRDGMMQGCNV 180

Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEA 236
           EAT  LA A  IPVIASGG+ ++ D++ L   +  GI GAI GRAIY+G LD+A A
Sbjct: 181 EATRELARAVSIPVIASGGVSSLEDVRSLAG-SPEGIAGAIVGRAIYDGGLDLATA 235


Lambda     K      H
   0.320    0.138    0.405 

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: 258
Number of extensions: 9
Number of successful extensions: 2
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: 247
Length of database: 246
Length adjustment: 24
Effective length of query: 223
Effective length of database: 222
Effective search space:    49506
Effective search space used:    49506
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 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate WP_011813891.1 HHAL_RS05570 (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.3476204.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-80  256.3   0.1    1.5e-80  256.1   0.1    1.0  1  NCBI__GCF_000015585.1:WP_011813891.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_011813891.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.1   0.1   1.5e-80   1.5e-80       1     229 [.       3     233 ..       3     235 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.1 bits;  conditional E-value: 1.5e-80
                             TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveel.e 72 
                                           +iPaiDlk+G++vrl qG++d +t+++ dp+++a ++ e gae+lH+VDLdgA +ge+ ++++i+ i+++  +
  NCBI__GCF_000015585.1:WP_011813891.1   3 VIPAIDLKNGHCVRLRQGRMDDETIFDADPVAVAGRWVEAGAERLHLVDLDGAVRGEPAHEQTIHAIARAYpD 75 
                                           89******************************************************************98647 PP

                             TIGR00007  73 vkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksel 145
                                           +++q+GGGiRs+e++ ++le+gv +vi+gt av++p++v+el +e+   +++v+lDa++g va+ GW+++se+
  NCBI__GCF_000015585.1:WP_011813891.1  76 TPLQIGGGIRSRETALRYLEAGVGYVIVGTRAVREPAFVEELCREIP-GRVCVGLDARGGYVATDGWEQTSEV 147
                                           89********************************************9.************************* PP

                             TIGR00007 146 slvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk..lgvkgvi 216
                                            +v+la+++e++g++++i+Tdi +dG+++G nve+t+el+++++++viasGGvss edv++l+    g++g+i
  NCBI__GCF_000015585.1:WP_011813891.1 148 AAVDLARRFEDAGVAALIFTDIGRDGMMQGCNVEATRELARAVSIPVIASGGVSSLEDVRSLAGspEGIAGAI 220
                                           ***************************************************************9889****** PP

                             TIGR00007 217 vGkAlyegklklk 229
                                           vG+A+y+g l+l 
  NCBI__GCF_000015585.1:WP_011813891.1 221 VGRAIYDGGLDLA 233
                                           ********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (246 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.07
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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