Alignments for a candidate for hisC in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Shewanella oneidensis MR-1

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate 201229 SO2072 histidinol-phosphate aminotransferase (NCBI ptt file)

Query= SwissProt::P06986
         (356 letters)



>FitnessBrowser__MR1:201229
          Length = 391

 Score =  302 bits (773), Expect = 1e-86
 Identities = 166/354 (46%), Positives = 227/354 (64%), Gaps = 13/354 (3%)

Query: 9   LARENVRNLTPYQSARRLGGNGDVWLNANEYP----TAVEFQLTQQTLNRYPECQPKAVI 64
           LAR  +  LTPYQSARRLGG GD+W+NANE P       E  LT+  LNRYPECQP A+I
Sbjct: 43  LARPELLELTPYQSARRLGGKGDIWINANESPFNNVAVGELDLTK--LNRYPECQPPALI 100

Query: 65  ENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVEC 124
             Y+QY+GV   +++ SRGADE IELLIRAFC PG D+I    PTYGMY++SA+T  V  
Sbjct: 101 NAYSQYSGVVESKIVASRGADEAIELLIRAFCIPGIDSIATFGPTYGMYAISAQTFNVGV 160

Query: 125 RTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAIVVAD 184
           + +     + L     +    G K+V++C+PNNPTG +I+       ++     +IVV D
Sbjct: 161 KALSLSAEYGLPAD-FATAARGAKLVFICNPNNPTGTVIDKARIEQAIQALPD-SIVVVD 218

Query: 185 EAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAPYP 244
           EAYIEFCP+ S+A  L  YP+L +LRTLSKAFALAG RCGF LANEE+I ++M+VIAPYP
Sbjct: 219 EAYIEFCPEYSVADLLETYPNLVVLRTLSKAFALAGARCGFLLANEEIIEIIMRVIAPYP 278

Query: 245 LSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVE---QVFDSETNYIL 301
           +  PV+++A QALSP GI  M+ +V ++  + E L AAL  + C +    V     NY+L
Sbjct: 279 VPLPVSEVAEQALSPAGIARMKTQVKELNTQGERLAAAL-NLYCEQWGGAVLKPNGNYVL 337

Query: 302 ARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQ 355
           A F   + V K L D GI+ R   K P L+  +R +  ++ ++ R++    +++
Sbjct: 338 AEFDDVAKVAKLLTDNGIVAR-AYKDPRLAKAIRFSFSSQVDTDRLVSLFESQK 390


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: 403
Number of extensions: 17
Number of successful extensions: 5
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: 391
Length adjustment: 30
Effective length of query: 326
Effective length of database: 361
Effective search space:   117686
Effective search space used:   117686
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 201229 SO2072 (histidinol-phosphate aminotransferase (NCBI ptt file))
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.12169.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    4.6e-99  317.5   0.0    5.3e-99  317.3   0.0    1.0  1  lcl|FitnessBrowser__MR1:201229  SO2072 histidinol-phosphate amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201229  SO2072 histidinol-phosphate aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.3   0.0   5.3e-99   5.3e-99       1     347 [.      45     387 ..      45     389 .. 0.94

  Alignments for each domain:
  == domain 1  score: 317.3 bits;  conditional E-value: 5.3e-99
                       TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenillgn 79 
                                     r+++ +l+pYq+ ar+lg+k++++ n+nE+Pf++   ++ +l+  l+kl+rYp++q+ +l +a+++y gv e +i++++
  lcl|FitnessBrowser__MR1:201229  45 RPELLELTPYQS-ARRLGGKGDIWINANESPFNNV--AVGELD--LTKLNRYPECQPPALINAYSQYSGVVESKIVASR 118
                                     678999******.9*******************99..677775..55******************************** PP

                       TIGR01141  80 Gsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPnnPtG 157
                                     G+de+ielliraf+ pg d+++++ pty mY++sa++ ++ vk  +l ++     ++++ +a++ +klvf+++PnnPtG
  lcl|FitnessBrowser__MR1:201229 119 GADEAIELLIRAFCIPGiDSIATFGPTYGMYAISAQTFNVGVKALSLSAE-YGLPADFA-TAARGAKLVFICNPNNPTG 195
                                     *************************************************9.46777777.8999*************** PP

                       TIGR01141 158 nllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvr 236
                                     ++++++ ie+ +++  d +VVvDeAYieF++e+sv++ll+ ypnlvvlrTlSKaf+LAg R+G+++an+eiie++++v+
  lcl|FitnessBrowser__MR1:201229 196 TVIDKARIEQAIQALPDSIVVVDEAYIEFCPEYSVADLLETYPNLVVLRTLSKAFALAGARCGFLLANEEIIEIIMRVI 274
                                     **************99*************************************************************** PP

                       TIGR01141 237 apynvsslaleaavaalrdsd..kiektveevkkererlleelkklegle...vyeSkaNFvlikvkedaeellealle 310
                                     apy+v+ +++e+a +al+ +    ++ +v+e++ + erl ++l+  ++     v + ++N+vl++++ d +++++ l++
  lcl|FitnessBrowser__MR1:201229 275 APYPVPLPVSEVAEQALSPAGiaRMKTQVKELNTQGERLAAALNLYCEQWggaVLKPNGNYVLAEFD-DVAKVAKLLTD 352
                                     ********************9999*******************97754322359999*********9.*********** PP

                       TIGR01141 311 kgiivRdlksaeglleeclRitvGtreenerllealk 347
                                     +gi+ R  k   + l +++R +  ++ +++rl+  ++
  lcl|FitnessBrowser__MR1:201229 353 NGIVARAYKD--PRLAKAIRFSFSSQVDTDRLVSLFE 387
                                     ********94..468***********99999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (391 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: 00:00:00.01
# Mc/sec: 9.36
//
[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