Alignments for a candidate for hisN in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Echinicola vietnamensis KMM 6221, DSM 17526

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate Echvi_2457 Echvi_2457 histidinol-phosphatase

Query= SwissProt::D2QPE6
         (382 letters)



>FitnessBrowser__Cola:Echvi_2457
          Length = 365

 Score =  520 bits (1338), Expect = e-152
 Identities = 257/382 (67%), Positives = 294/382 (76%), Gaps = 17/382 (4%)

Query: 1   MQKIVFIDRDGTLIAEPQPDQQVDSLAKLDFIPKAISAMRKIAEDTTYELVMVTNQDGLG 60
           M+K++FIDRDGT+I EP  D QVDSL KL+F PKAIS +RKIAE+T YELVMVTNQDGLG
Sbjct: 1   MKKVLFIDRDGTIIKEPPVDYQVDSLEKLEFYPKAISNLRKIAEETDYELVMVTNQDGLG 60

Query: 61  TGSFPEDTFWPAHNKMMSTFAGENVNFAAVHIDRHFPHDNSSTRKPGVGMLTQYFEASYD 120
           T SFPEDTFWPA  KM+ T   E V F+A+HID+ F H+N+ TRKP  G+LT Y +  YD
Sbjct: 61  TDSFPEDTFWPAQYKMLKTLEEEGVVFSAIHIDKTFEHENAPTRKPRTGLLTDYLKGDYD 120

Query: 121 LTNSFVIGDRLTDVQLAVNLGAKAILFMPPNGLAAVQSADVSGLTEAMKQAIVLQTGDWD 180
           L +SFVIGDR TDVQLA NLG +AI                  + E   +   L T  WD
Sbjct: 121 LAHSFVIGDRKTDVQLAKNLGTQAIF-----------------IGEEAAEGAALSTTSWD 163

Query: 181 EIYEFLRLPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADL 240
           EIYEFLRLP+R   V+R+T ETQI + +NLDG G+  + TGL FFDHML+Q+ KH G DL
Sbjct: 164 EIYEFLRLPSRIGQVKRSTSETQIEIMVNLDGSGKCQIDTGLPFFDHMLEQLGKHGGTDL 223

Query: 241 AIHVNGDLHIDEHHTIEDTALALGEAYRRALGDKRGISRYGFLLPMDEALAQVGIDFSGR 300
            I VNGDLHIDEHHTIEDTALALGEAY +ALGDK+GI RYGFLLPMD+ LAQV IDF GR
Sbjct: 224 DIKVNGDLHIDEHHTIEDTALALGEAYLKALGDKKGIYRYGFLLPMDDVLAQVAIDFGGR 283

Query: 301 PWLVWDAEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIKVEGDNEHHKIEAIFKAFAKA 360
           PW++W+AEF REKIGDMPTEMFYHFFKSFSDTA CNLNIK EG NEHHKIEAIFK  A+A
Sbjct: 284 PWMMWEAEFNREKIGDMPTEMFYHFFKSFSDTAKCNLNIKAEGANEHHKIEAIFKGLARA 343

Query: 361 IKMAVRRDINELDNLPSTKGVL 382
           IKMAV+RDI  L+ LPSTKGVL
Sbjct: 344 IKMAVKRDIAALNQLPSTKGVL 365


Lambda     K      H
   0.320    0.136    0.403 

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: 472
Number of extensions: 22
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: 382
Length of database: 365
Length adjustment: 30
Effective length of query: 352
Effective length of database: 335
Effective search space:   117920
Effective search space used:   117920
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: 50 (23.9 bits)

Align candidate Echvi_2457 Echvi_2457 (histidinol-phosphatase)
to HMM TIGR01261 (hisB: histidinol-phosphatase (EC 3.1.3.15))

# 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/TIGR01261.hmm
# target sequence database:        /tmp/gapView.12065.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01261  [M=161]
Accession:   TIGR01261
Description: hisB_Nterm: histidinol-phosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    2.5e-57  179.0   0.0    3.7e-57  178.4   0.0    1.3  1  lcl|FitnessBrowser__Cola:Echvi_2457  Echvi_2457 histidinol-phosphatas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2457  Echvi_2457 histidinol-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4   0.0   3.7e-57   3.7e-57       1     152 [.       2     153 ..       2     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 3.7e-57
                            TIGR01261   1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklk.eagyklvlvtnqdGlGtesfPkedfdkphal 73 
                                          +k+lfidrdGt+i+eP+ d+qvd+lekl++ +k+i++l+k+  e++y+lv+vtnqdGlGt+sfP++ f  ++ +
  lcl|FitnessBrowser__Cola:Echvi_2457   2 KKVLFIDRDGTIIKEPPVDYQVDSLEKLEFYPKAISNLRKIAeETDYELVMVTNQDGLGTDSFPEDTFWPAQYK 75 
                                          589*************************************962689**************************** PP

                            TIGR01261  74 mlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkyk 147
                                          ml+ ++ eG+vf+ + i++ f+++n+ +rkP+++ll++yl k ++d ++s+viGdr+td+qla+nlg +++   
  lcl|FitnessBrowser__Cola:Echvi_2457  76 MLKTLEEEGVVFSAIHIDKTFEHENAPTRKPRTGLLTDYL-KGDYDLAHSFVIGDRKTDVQLAKNLGTQAIFIG 148
                                          ****************************************.678*************************99887 PP

                            TIGR01261 148 eeeln 152
                                          ee  +
  lcl|FitnessBrowser__Cola:Echvi_2457 149 EEAAE 153
                                          77654 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (365 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: 14.70
//
[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