Alignments for a candidate for hisC in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Phaeobacter inhibens BS107

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate GFF2492 PGA1_c25240 histidinol-phosphate aminotransferase HisC

Query= reanno::Phaeo:GFF2492
         (361 letters)



>FitnessBrowser__Phaeo:GFF2492
          Length = 361

 Score =  721 bits (1861), Expect = 0.0
 Identities = 361/361 (100%), Positives = 361/361 (100%)

Query: 1   MTHIAPQPGILDIALYEGGAAHVKGMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYP 60
           MTHIAPQPGILDIALYEGGAAHVKGMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYP
Sbjct: 1   MTHIAPQPGILDIALYEGGAAHVKGMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYP 60

Query: 61  SSDHSGLRQAIGEVYGLPMEQIICGAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISA 120
           SSDHSGLRQAIGEVYGLPMEQIICGAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISA
Sbjct: 61  SSDHSGLRQAIGEVYGLPMEQIICGAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISA 120

Query: 121 LAAGATPVEVAERDRVTDVDALLAGCTERTRLVFIANPNNPTGTMIGMADLARLADGLPK 180
           LAAGATPVEVAERDRVTDVDALLAGCTERTRLVFIANPNNPTGTMIGMADLARLADGLPK
Sbjct: 121 LAAGATPVEVAERDRVTDVDALLAGCTERTRLVFIANPNNPTGTMIGMADLARLADGLPK 180

Query: 181 GALLVLDGAYAEYVEGYDAGAALVANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVL 240
           GALLVLDGAYAEYVEGYDAGAALVANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVL
Sbjct: 181 GALLVLDGAYAEYVEGYDAGAALVANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVL 240

Query: 241 NRVRGPFNLSSTALAGAEAAVRDTDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFI 300
           NRVRGPFNLSSTALAGAEAAVRDTDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFI
Sbjct: 241 NRVRGPFNLSSTALAGAEAAVRDTDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFI 300

Query: 301 LARFASPEEAGACDAFLQSRGLIVRRVTGYKLPAALRITVGDETACNALVAAMKVFKDGP 360
           LARFASPEEAGACDAFLQSRGLIVRRVTGYKLPAALRITVGDETACNALVAAMKVFKDGP
Sbjct: 301 LARFASPEEAGACDAFLQSRGLIVRRVTGYKLPAALRITVGDETACNALVAAMKVFKDGP 360

Query: 361 A 361
           A
Sbjct: 361 A 361


Lambda     K      H
   0.318    0.134    0.399 

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: 635
Number of extensions: 13
Number of successful extensions: 1
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: 361
Length of database: 361
Length adjustment: 29
Effective length of query: 332
Effective length of database: 332
Effective search space:   110224
Effective search space used:   110224
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate GFF2492 PGA1_c25240 (histidinol-phosphate aminotransferase HisC)
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.27411.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    4.1e-97  311.1   0.0    4.7e-97  310.9   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2492  PGA1_c25240 histidinol-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2492  PGA1_c25240 histidinol-phosphate aminotransferase HisC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.9   0.0   4.7e-97   4.7e-97       3     347 ..       9     354 ..       7     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 310.9 bits;  conditional E-value: 4.7e-97
                          TIGR01141   3 kikklepYqpg.arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenill 77 
                                         i +++ Y+ g a+ +g ++v kL+snEnP+gps+k++ea++++++++hrYp+++++ l++a+ +++g+ +e+i+ 
  lcl|FitnessBrowser__Phaeo:GFF2492   9 GILDIALYEGGaAHVKGMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYPSSDHSGLRQAIGEVYGLPMEQIIC 84 
                                        57788999999555566669******************************************************** PP

                          TIGR01141  78 gnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPn 153
                                        g+Gsde+i++l++a++ pgd+vl++e+ ++mY++sa +aga  +ev+ ++    d++a+l+  +e+++lvf+a+Pn
  lcl|FitnessBrowser__Phaeo:GFF2492  85 GAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISALAAGATPVEVAERDR-VTDVDALLAGCTERTRLVFIANPN 159
                                        **********************************************98888.69********************** PP

                          TIGR01141 154 nPtGnllkreeiekvleev.edalVVvDeAYieFsee.asvlellaeypnlvvlrTlSKafgLAglRvGyaianae 227
                                        nPtG+++  +++ ++++   + al V+D AY e+ e     + l+a+++n+v++rT+SK++gL+g RvG ++a + 
  lcl|FitnessBrowser__Phaeo:GFF2492 160 NPTGTMIGMADLARLADGLpKGALLVLDGAYAEYVEGyDAGAALVANRDNVVMTRTFSKIYGLGGARVGWGYAPKP 235
                                        *******************88***************9455799********************************* PP

                          TIGR01141 228 iiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvke.dae 302
                                        ii++l++vr p+n+ss al+ a aa+rd d++e++ +e++k r++l e+l++l g+    S aNF+l+++ + +++
  lcl|FitnessBrowser__Phaeo:GFF2492 236 IIDVLNRVRGPFNLSSTALAGAEAAVRDTDYTEHCRKENAKWRTWLAEALAEL-GVPSDTSCANFILARFASpEEA 310
                                        *****************************************************.8***************998555 PP

                          TIGR01141 303 ellea.llekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                         +++a l  +g+ivR ++ ++  l+ +lRitvG +  +++l++a+k
  lcl|FitnessBrowser__Phaeo:GFF2492 311 GACDAfLQSRGLIVRRVTGYK--LPAALRITVGDETACNALVAAMK 354
                                        5555516678**********4..6*****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (361 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: 8.29
//
[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