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

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.12071.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.11
//
[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:

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