Alignments for a candidate for hisC in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Shewanella sp. ANA-3

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate 7024674 Shewana3_1852 histidinol phosphate aminotransferase (RefSeq)

Query= SwissProt::P06986
         (356 letters)



>FitnessBrowser__ANA3:7024674
          Length = 401

 Score =  303 bits (775), Expect = 7e-87
 Identities = 165/359 (45%), Positives = 227/359 (63%), Gaps = 9/359 (2%)

Query: 3   TVTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYP--TAVEFQLTQQTLNRYPECQP 60
           T     LAR  +  LTPYQSARRLGG GD+W+NANE P       +L    LNRYPECQP
Sbjct: 47  TTLAARLARPELLELTPYQSARRLGGRGDIWINANESPFNNVAVAELDLSKLNRYPECQP 106

Query: 61  KAVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETI 120
            A+I  Y+QY+GV   +++ SRGADE IELLIRAFC PG D+I    PTYGMY++SA+T 
Sbjct: 107 PALINAYSQYSGVVESKIVASRGADEAIELLIRAFCVPGIDSIATFGPTYGMYAISAQTF 166

Query: 121 GVECRTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAI 180
            V  + +     + L     +    G K+V++C+PNNPTG +I+       ++     AI
Sbjct: 167 NVGVKALSLTAEYGLPAD-FATAARGAKLVFICNPNNPTGTVIDKARIEQAIQALPD-AI 224

Query: 181 VVADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVI 240
           VV DEAYIEFCP+ S+A  L  YP+L +LRTLSKAFALAG RCGF LANEE+I ++M+VI
Sbjct: 225 VVVDEAYIEFCPEYSVADLLESYPNLVVLRTLSKAFALAGARCGFLLANEEIIEIIMRVI 284

Query: 241 APYPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVE---QVFDSET 297
           APYP+  PV+++A QALS  GI  M+ +V ++ A+ E L AAL  + C +    V     
Sbjct: 285 APYPVPLPVSEVAVQALSAAGIARMKTQVKELNAQGERLAAAL-NLYCEQWGGAVLTPNG 343

Query: 298 NYILARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQV 356
           NY+LA F   + V + L D GI+ R   K P L+  +R +  ++ ++ R++    ++++
Sbjct: 344 NYVLAEFDDVAKVAQLLIDNGIVAR-AYKDPRLAKAIRFSFSSQADTDRLVSLFESQKL 401


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: 413
Number of extensions: 19
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: 401
Length adjustment: 30
Effective length of query: 326
Effective length of database: 371
Effective search space:   120946
Effective search space used:   120946
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 7024674 Shewana3_1852 (histidinol phosphate aminotransferase (RefSeq))
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.25602.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.8e-101  323.8   0.0   6.8e-101  323.6   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7024674  Shewana3_1852 histidinol phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024674  Shewana3_1852 histidinol phosphate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.6   0.0  6.8e-101  6.8e-101       1     347 [.      55     397 ..      55     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 323.6 bits;  conditional E-value: 6.8e-101
                         TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenill 77 
                                       r+++ +l+pYq+ ar+lg+ ++++ n+nE+Pf++   ++++l   l+kl+rYp++q+ +l +a+++y gv e +i++
  lcl|FitnessBrowser__ANA3:7024674  55 RPELLELTPYQS-ARRLGGRGDIWINANESPFNNV--AVAEL--DLSKLNRYPECQPPALINAYSQYSGVVESKIVA 126
                                       678999******.9*******************99..56666..455****************************** PP

                         TIGR01141  78 gnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPn 153
                                       ++G+de+ielliraf+ pg d+++++ pty mY++sa++ ++ vk  +l+++     ++++ +a++ +klvf+++Pn
  lcl|FitnessBrowser__ANA3:7024674 127 SRGADEAIELLIRAFCVPGiDSIATFGPTYGMYAISAQTFNVGVKALSLTAE-YGLPADFA-TAARGAKLVFICNPN 201
                                       ****************************************************.46777777.8999*********** PP

                         TIGR01141 154 nPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiie 230
                                       nPtG++++++ ie+ +++  da+VVvDeAYieF++e+sv++ll+ ypnlvvlrTlSKaf+LAg R+G+++an+eiie
  lcl|FitnessBrowser__ANA3:7024674 202 NPTGTVIDKARIEQAIQALPDAIVVVDEAYIEFCPEYSVADLLESYPNLVVLRTLSKAFALAGARCGFLLANEEIIE 278
                                       ******************99********************************************************* PP

                         TIGR01141 231 alekvrapynvsslaleaavaalrdsd..kiektveevkkererlleelkklegle...vyeSkaNFvlikvkedae 302
                                       ++++v+apy+v+ +++e+av+al+ +    ++ +v+e++++ erl ++l+  ++     v   ++N+vl++++ d +
  lcl|FitnessBrowser__ANA3:7024674 279 IIMRVIAPYPVPLPVSEVAVQALSAAGiaRMKTQVKELNAQGERLAAALNLYCEQWggaVLTPNGNYVLAEFD-DVA 354
                                       **************************9999*******************97753322348889*********9.*** PP

                         TIGR01141 303 elleallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                       ++++ l+++gi+ R  k   + l +++R +  ++ +++rl+  ++
  lcl|FitnessBrowser__ANA3:7024674 355 KVAQLLIDNGIVARAYKD--PRLAKAIRFSFSSQADTDRLVSLFE 397
                                       ****************94..468****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (401 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: 13.28
//
[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