GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Dyella japonica UNC79MFTsu3.2

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate N515DRAFT_2936 N515DRAFT_2936 histidinol-phosphate aminotransferase

Query= SwissProt::P06986
         (356 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2936
          Length = 353

 Score =  272 bits (695), Expect = 1e-77
 Identities = 151/353 (42%), Positives = 210/353 (59%), Gaps = 2/353 (0%)

Query: 4   VTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQPKAV 63
           +++ DLAR  +R + PY SAR     G + LNANE   A   +   +  NRYP+ QP A+
Sbjct: 1   MSVLDLARPELRAMQPYSSARMEASGGAILLNANESAWAPAGE-AGRGCNRYPDPQPAAL 59

Query: 64  IENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVE 123
           +   A   GV+ EQ+LV RG+DE I+LL+RAFC  G+DAI   PPT+GMYSV A      
Sbjct: 60  LRALAALYGVREEQLLVGRGSDEAIDLLVRAFCRAGRDAIAIQPPTFGMYSVCARIQDAG 119

Query: 124 CRTVPTLDNWQLDLQGISDKLD-GVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAIVV 182
              VP   ++ +D   +   L   VK+V+VC+PNNPTGQ +       L     G+A++V
Sbjct: 120 IVEVPLAADFTVDADALLAALTPAVKLVFVCTPNNPTGQPVPRATIERLARELAGRALLV 179

Query: 183 ADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAP 242
            DEAY+EF    S+AG +  Y +LA+LRTLSKA+ALAG R G  LA+ EVI LL K+I P
Sbjct: 180 VDEAYVEFADGGSVAGLIDTYDNLAVLRTLSKAWALAGARIGTLLAHAEVIALLRKIIPP 239

Query: 243 YPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYILA 302
           YPL  P    A + LS QG     E +  + AER  +  AL  +P V +V  S+ N++  
Sbjct: 240 YPLPLPCVTAALEGLSAQGQAEAAEHIRIVRAERARMTPALAALPGVREVLPSQANFLAV 299

Query: 303 RFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQ 355
           RF  + A ++ L+  GI++RD  + P+L   LRIT+GT  E+ RV+D L  ++
Sbjct: 300 RFDDAGAAYQRLFAAGIVVRDVRRYPNLGDALRITIGTPAENARVLDVLNGDR 352


Lambda     K      H
   0.319    0.135    0.396 

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: 342
Number of extensions: 12
Number of successful extensions: 3
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: 356
Length of database: 353
Length adjustment: 29
Effective length of query: 327
Effective length of database: 324
Effective search space:   105948
Effective search space used:   105948
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: 49 (23.5 bits)

Align candidate N515DRAFT_2936 N515DRAFT_2936 (histidinol-phosphate aminotransferase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.1404662.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-109  352.6   0.0   1.2e-109  352.4   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936  N515DRAFT_2936 histidinol-phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2936  N515DRAFT_2936 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.4   0.0  1.2e-109  1.2e-109       1     347 [.       8     349 ..       8     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 1.2e-109
                                    TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealak 66 
                                                  r+++++++pY++ ar  +  + + Ln+nE++++p      ++    +  +rYpdpq+++l +ala+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936   8 RPELRAMQPYSS-ARMEASGGAILLNANESAWAPAG----EA---GRGCNRYPDPQPAALLRALAA 65 
                                                  789*********.78888889*************93....33...3468***************** PP

                                    TIGR01141  67 ylgveeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqe 131
                                                   +gv ee++l+g+Gsde+i+ll+raf+  g da+++ +pt+ mY+v+a+i++a ++evpl++d++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936  66 LYGVREEQLLVGRGSDEAIDLLVRAFCRAGrDAIAIQPPTFGMYSVCARIQDAGIVEVPLAADFTV 131
                                                  ******************************9*********************************** PP

                                    TIGR01141 132 dleavleaakekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFseeasvlell 196
                                                  d +a+l+a +  vklvf+++PnnPtG+ + r+ ie+++ e + +al VvDeAY+eF++  sv+ l+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936 132 DADALLAALTPAVKLVFVCTPNNPTGQPVPRATIERLARELAgRALLVVDEAYVEFADGGSVAGLI 197
                                                  *****************************************55*********************** PP

                                    TIGR01141 197 aeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsd..kie 260
                                                    y+nl+vlrTlSKa +LAg R+G ++a+ae+i  l+k+++py+++ ++++aa++ l+ +   + +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936 198 DTYDNLAVLRTLSKAWALAGARIGTLLAHAEVIALLRKIIPPYPLPLPCVTAALEGLSAQGqaEAA 263
                                                  **********************************************************99977889 PP

                                    TIGR01141 261 ktveevkkererlleelkklegle.vyeSkaNFvlikvkedaeelleallekgiivRdlksaegll 325
                                                  + ++ v++er+r++ +l++l+g++ v +S+aNF+ ++++ da +++++l  +gi+vRd++ +++ l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936 264 EHIRIVRAERARMTPALAALPGVReVLPSQANFLAVRFD-DAGAAYQRLFAAGIVVRDVRRYPN-L 327
                                                  99************************************9.**********************88.5 PP

                                    TIGR01141 326 eeclRitvGtreenerllealk 347
                                                   ++lRit+Gt+ en r+l++l+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2936 328 GDALRITIGTPAENARVLDVLN 349
                                                  ******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (353 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: 15.94
//
[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