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

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.19707.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.49
//
[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