GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Shewanella loihica PV-4

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 5209749 Shew_2202 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)

Query= ecocyc::PRIBFAICARPISOM-MONOMER
         (245 letters)



>FitnessBrowser__PV4:5209749
          Length = 245

 Score =  295 bits (754), Expect = 7e-85
 Identities = 145/245 (59%), Positives = 181/245 (73%)

Query: 1   MIIPALDLIDGTVVRLHQGDYGKQRDYGNDPLPRLQDYAAQGAEVLHLVDLTGAKDPAKR 60
           MIIPA+DLI+G VVRL+QGDY +Q  +   PL +LQ Y AQGA  LH+VDLTGAKDP +R
Sbjct: 1   MIIPAIDLIEGQVVRLYQGDYAQQTTFDLSPLAQLQAYQAQGATWLHIVDLTGAKDPDRR 60

Query: 61  QIPLIKTLVAGVNVPVQVGGGVRSEEDVAALLEAGVARVVVGSTAVKSQDMVKGWFERFG 120
           Q  LI  LV  +   +QVGGG+RSE  V  LL+ GV RVV+GS AVK  ++V+ W E +G
Sbjct: 61  QTRLIGELVENLEANIQVGGGIRSEAQVKELLDLGVKRVVIGSLAVKQPELVQSWLETYG 120

Query: 121 ADALVLALDVRIDEQGNKQVAVSGWQENSGVSLEQLVETYLPVGLKHVLCTDISRDGTLA 180
           +DA+ LALDV I++ G K VAVSGWQ   G +LE LV T+ P GLKH L TDISRDGTL 
Sbjct: 121 SDAICLALDVNINQAGEKIVAVSGWQSGGGKTLESLVATFAPYGLKHALVTDISRDGTLQ 180

Query: 181 GSNVSLYEEVCARYPQVAFQSSGGIGDIDDVAALRGTGVRGVIVGRALLEGKFTVKEAIA 240
           GSN  LY+E+ ARYP + +Q+SGGI  +DDV+A+R +G  G+I+G+ALL   FTV+EAIA
Sbjct: 181 GSNTQLYQEIVARYPDIEWQASGGIATLDDVSAVRNSGASGIIIGKALLINNFTVQEAIA 240

Query: 241 CWQNA 245
           CW NA
Sbjct: 241 CWPNA 245


Lambda     K      H
   0.318    0.137    0.397 

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: 193
Number of extensions: 4
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: 245
Length of database: 245
Length adjustment: 24
Effective length of query: 221
Effective length of database: 221
Effective search space:    48841
Effective search space used:    48841
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: 46 (22.3 bits)

Align candidate 5209749 Shew_2202 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq))
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.17113.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-79  253.1   0.8    1.5e-79  252.9   0.8    1.0  1  lcl|FitnessBrowser__PV4:5209749  Shew_2202 1-(5-phosphoribosyl)-5


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209749  Shew_2202 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazol
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.9   0.8   1.5e-79   1.5e-79       1     231 []       2     238 ..       2     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 252.9 bits;  conditional E-value: 1.5e-79
                        TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqvG 78 
                                      iiPaiDl+eG+vvrl+qGd++++t+++ +pl++ ++++++ga++lH+VDL+gAk+  ++++++i ++ve+le+++qvG
  lcl|FitnessBrowser__PV4:5209749   2 IIPAIDLIEGQVVRLYQGDYAQQTTFDLSPLAQLQAYQAQGATWLHIVDLTGAKDPDRRQTRLIGELVENLEANIQVG 79 
                                      8***************************************************************************** PP

                        TIGR00007  79 GGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakeg.....evavkGWkekselslvela 151
                                      GGiRs ++v++ll+lgv+rv+ig++av++pelv+++l+++gs+ i+++lD++ +      vav+GW+     +l++l+
  lcl|FitnessBrowser__PV4:5209749  80 GGIRSEAQVKELLDLGVKRVVIGSLAVKQPELVQSWLETYGSDAICLALDVNINqagekIVAVSGWQSGGGKTLESLV 157
                                      ***************************************************988777778****************** PP

                        TIGR00007 152 kkleelgleeiilTdiekdGtlsGvnveltkelvke.aeveviasGGvssiedvkalkklgvkgvivGkAlyegklkl 228
                                       +++ +gl++ ++Tdi++dGtl+G n++l++e+v++  ++e +asGG+++ +dv a++++g++g+i+GkAl+ +++++
  lcl|FitnessBrowser__PV4:5209749 158 ATFAPYGLKHALVTDISRDGTLQGSNTQLYQEIVARyPDIEWQASGGIATLDDVSAVRNSGASGIIIGKALLINNFTV 235
                                      ************************************9****************************************9 PP

                        TIGR00007 229 kea 231
                                      +ea
  lcl|FitnessBrowser__PV4:5209749 236 QEA 238
                                      985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (245 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: 9.37
//
[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