GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Thermophagus xiamenensis HS1

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_010527280.1 GQW_RS0106955 bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB

Query= SwissProt::Q8ABA7
         (374 letters)



>NCBI__GCF_000220155.1:WP_010527280.1
          Length = 378

 Score =  526 bits (1355), Expect = e-154
 Identities = 256/375 (68%), Positives = 303/375 (80%), Gaps = 4/375 (1%)

Query: 3   KKILFIDRDGTLVIEPPIDYQLDSLEKLEFYPRVFRNLGFIRSKLDFEFVMVTNQDGLGT 62
           K+ILFIDRDGT++ EPPIDYQ+DSLEKLEFYP V  NL  I   LDF+ VMVTNQDGLGT
Sbjct: 5   KRILFIDRDGTIIKEPPIDYQVDSLEKLEFYPGVMVNLARIVRHLDFQLVMVTNQDGLGT 64

Query: 63  SSFPEDTFWPAHNLMLKTLAGEGITFDDILIDRSFPEDNAPTRKPRTGMLTKYIDNPEYD 122
            SFPE+TFWPAHN ML+TL GEGI F  I IDRSFPEDNAPTRKPRTGML  Y+    YD
Sbjct: 65  PSFPEETFWPAHNKMLETLKGEGIQFSAIHIDRSFPEDNAPTRKPRTGMLKDYLSG-NYD 123

Query: 123 LAESFVIGDRPTDVELAKNLGCRAIYL---QEATDDLKEKGLEEVCALATTDWDQVAEFL 179
           L  SFVIGDR TDVELAKN+GC+AI +   +EA   L+E+ L+  C L +T W+++A++L
Sbjct: 124 LDNSFVIGDRLTDVELAKNMGCKAILMKKPEEAIPLLEEQNLKNYCVLCSTRWEEIADYL 183

Query: 180 FAGERKAEVRRTTKETDIYVSLNLDGNGGCDISTGLGFFDHMLEQIGKHSGMDLTIRVKG 239
           F  ER+  V R T ET I V+LNLDG G CDISTGLGFFDHMLEQIG+HSG DL I+V G
Sbjct: 184 FTKERQVTVERNTSETKIKVTLNLDGTGSCDISTGLGFFDHMLEQIGRHSGCDLQIKVTG 243

Query: 240 DLEVDEHHTIEDTAIALGECIYQALGSKRGIERYGYALPMDDCLCQVCLDFGGRPWLVWD 299
           DL VDEHHTIEDTA+ALGE + +ALG KRGIERYG++LPMDDC+  V +DFGGRPWLVW 
Sbjct: 244 DLHVDEHHTIEDTALALGEALKKALGDKRGIERYGFSLPMDDCMAHVAIDFGGRPWLVWK 303

Query: 300 AEFNREKIGEMPTEMFLHFFKSLSDAAKMNLNIKAEGQNEHHKIEGIFKALARALKMALK 359
           A+F REK+G++PTEMF HFFKSL+DAA  N+ IKA+G+NEHHKIE IFKALARA+K A++
Sbjct: 304 AKFKREKVGDLPTEMFYHFFKSLADAAAANIYIKAKGKNEHHKIEAIFKALARAIKAAIR 363

Query: 360 RDIYHFELPSSKGVL 374
           +D  + +LPS+KG L
Sbjct: 364 KDPLNRQLPSTKGFL 378


Lambda     K      H
   0.321    0.140    0.422 

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: 463
Number of extensions: 23
Number of successful extensions: 4
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: 374
Length of database: 378
Length adjustment: 30
Effective length of query: 344
Effective length of database: 348
Effective search space:   119712
Effective search space used:   119712
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 WP_010527280.1 GQW_RS0106955 (bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB)
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.3558987.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.1e-58  181.0   0.0    9.3e-58  180.4   0.0    1.3  1  NCBI__GCF_000220155.1:WP_010527280.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010527280.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.4   0.0   9.3e-58   9.3e-58       2     150 ..       6     154 ..       5     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 9.3e-58
                             TIGR01261   2 kilfidrdGtlieePksdfqvdaleklklekkvipallkl.keagyklvlvtnqdGlGtesfPkedfdkphal 73 
                                           +ilfidrdGt+i+eP+ d+qvd+lekl++ ++v+ +l ++ ++++++lv+vtnqdGlGt+sfP+e f  +h++
  NCBI__GCF_000220155.1:WP_010527280.1   6 RILFIDRDGTIIKEPPIDYQVDSLEKLEFYPGVMVNLARIvRHLDFQLVMVTNQDGLGTPSFPEETFWPAHNK 78 
                                           79***********************************9973679***************************** PP

                             TIGR01261  74 mlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglky 146
                                           ml+ +k eGi+f+ + i+++f+edn+ +rkP++++l++yl + ++d ++s+viGdr td++la+n+g +++ +
  NCBI__GCF_000220155.1:WP_010527280.1  79 MLETLKGEGIQFSAIHIDRSFPEDNAPTRKPRTGMLKDYL-SGNYDLDNSFVIGDRLTDVELAKNMGCKAILM 150
                                           ****************************************.778**************************998 PP

                             TIGR01261 147 keee 150
                                           k++e
  NCBI__GCF_000220155.1:WP_010527280.1 151 KKPE 154
                                           8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (378 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: 22.06
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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