Aligments for a candidate for hisC in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Aligments for a candidate for hisC in Paraburkholderia bryophila 376MFSha3.1

Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate H281DRAFT_05654 H281DRAFT_05654 histidinol phosphate aminotransferase apoenzyme

Query= curated2:Q46WL3
         (366 letters)



>FitnessBrowser__Burk376:H281DRAFT_05654
          Length = 356

 Score =  461 bits (1185), Expect = e-134
 Identities = 236/348 (67%), Positives = 275/348 (79%), Gaps = 4/348 (1%)

Query: 12  IIRDDVRAMGAYHVPDSHGLVKLDAMENPYRLPPALRSELAARLGEVALNRYPVPSSEAL 71
           IIR DV AM +Y V D+ G +KLDAMENP+ LPP L + L   L  VALNRYP P  EAL
Sbjct: 7   IIRRDVLAMTSYPVADATGYIKLDAMENPFPLPPVLAAHLGEHLAGVALNRYPAPRPEAL 66

Query: 72  RAKLKEVMQVPAGMEVLLGNGSDEIISMLALAAARPGAKVMAPVPGFVMYAMSAQFAGLE 131
             K+K VM VPAG +VLLGNGSDEIISM+++A A+PGAKV+APVPGFVMY MSA+ A LE
Sbjct: 67  IEKIKRVMGVPAGCDVLLGNGSDEIISMVSIACAKPGAKVLAPVPGFVMYQMSAKLANLE 126

Query: 132 FVGVPLRADFTLDRGAMLAAMAEHQPAIVYLAYPNNPTGNLFDAADMEAIVRAAQGSVCR 191
           F+GVPL ADFTLD  AMLAA+AEH+PA+VYLAYPNNPTG LFD ADME I+ AA     +
Sbjct: 127 FIGVPLNADFTLDTEAMLAAIAEHEPAVVYLAYPNNPTGTLFDDADMERIIAAA----TK 182

Query: 192 SLVVVDEAYQPFAQESWMSRLTDFGNLLVMRTVSKLGLAGIRLGYVAGDPQWLEQLDKVR 251
           SLVV+DEAYQPFAQ SW+ R   F N++VMRTVSKLGLAGIRLGY+ G P WL +LDKVR
Sbjct: 183 SLVVIDEAYQPFAQRSWLPRADAFDNVVVMRTVSKLGLAGIRLGYLVGKPAWLTELDKVR 242

Query: 252 PPYNVNVLTEATALFALEHVAVLDEQAAQLRAERSRVAEGMAAHGGVTVFPSAANFLLAR 311
           PPYN NVLT+A A F L+HV VLD QAAQLR ER+++A+ +A   G  VFPSA NFLL R
Sbjct: 243 PPYNTNVLTQAAADFLLDHVDVLDSQAAQLRDERTKLAQAVAELPGAEVFPSAGNFLLVR 302

Query: 312 VPDAAQTFDRLLARKVLIKNVSKMHPLLANCLRVTVSTPEENAQFLEA 359
           VPDA+  F+ LLA +VLIKNVSKMH LLANC+R+TV +PEENAQ + A
Sbjct: 303 VPDASVLFETLLAARVLIKNVSKMHALLANCVRLTVGSPEENAQLIAA 350


Lambda     K      H
   0.321    0.134    0.382 

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: 426
Number of extensions: 13
Number of successful extensions: 2
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: 366
Length of database: 356
Length adjustment: 29
Effective length of query: 337
Effective length of database: 327
Effective search space:   110199
Effective search space used:   110199
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate H281DRAFT_05654 H281DRAFT_05654 (histidinol phosphate aminotransferase apoenzyme)
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.7606.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.5e-100  320.6   0.0   6.2e-100  320.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05654  H281DRAFT_05654 histidinol phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05654  H281DRAFT_05654 histidinol phosphate aminotransferase apoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.4   0.0  6.2e-100  6.2e-100       2     347 ..      10     352 ..       9     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 320.4 bits;  conditional E-value: 6.2e-100
                                    TIGR01141   2 ekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkeala 65 
                                                  +++ +++ Y  + +    ++ +kL+++EnPf+ ++ + ++l e+l+   l+rYp p + +l e++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05654  10 RDVLAMTSYPVA-D---ATGYIKLDAMENPFPLPPVLAAHLGEHLAgvALNRYPAPRPEALIEKIK 71 
                                                  667777777773.2...2368*************************999***************** PP

                                    TIGR01141  66 kylgvee.enillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgq 130
                                                  +++gv +  ++llgnGsde+i+++  a+++pg++vl++ p + mY++sak+a+ e + vpl++d++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05654  72 RVMGVPAgCDVLLGNGSDEIISMVSIACAKPGAKVLAPVPGFVMYQMSAKLANLEFIGVPLNADFT 137
                                                  ****765269*******************************************************9 PP

                                    TIGR01141 131 edleavle.aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlel 195
                                                   d+ea+l+ +a++++ +v+la+PnnPtG+l++ +++e++++++++ lVV+DeAY  F+++ s+l+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05654 138 LDTEAMLAaIAEHEPAVVYLAYPNNPTGTLFDDADMERIIAAATKSLVVIDEAYQPFAQR-SWLPR 202
                                                  *****999678899****************************99***************6.***** PP

                                    TIGR01141 196 laeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiek 261
                                                  +  ++n+vv+rT+SK+  LAg+R+Gy+++++++  +l+kvr+pyn+++l+++aa   l++ d + +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05654 203 ADAFDNVVVMRTVSKLG-LAGIRLGYLVGKPAWLTELDKVRPPYNTNVLTQAAADFLLDHVDVLDS 267
                                                  ***************86.************************************************ PP

                                    TIGR01141 262 tveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaegllee 327
                                                  + ++++ er+ l +++++l+g ev++S +NF+l++v+ da+ l+e+ll ++++++++++++ ll +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05654 268 QAAQLRDERTKLAQAVAELPGAEVFPSAGNFLLVRVP-DASVLFETLLAARVLIKNVSKMHALLAN 332
                                                  *************************************.**************************** PP

                                    TIGR01141 328 clRitvGtreenerllealk 347
                                                  c+R+tvG++een +l++alk
  lcl|FitnessBrowser__Burk376:H281DRAFT_05654 333 CVRLTVGSPEENAQLIAALK 352
                                                  *****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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: 11.89
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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