GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Pseudomonas stutzeri RCH2

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate GFF1942 Psest_1985 histidinol-phosphate aminotransferase

Query= metacyc::BSU22620-MONOMER
         (360 letters)



>FitnessBrowser__psRCH2:GFF1942
          Length = 369

 Score =  288 bits (737), Expect = 2e-82
 Identities = 157/356 (44%), Positives = 220/356 (61%), Gaps = 3/356 (0%)

Query: 7   LKQLKPYQPGKPIEAVKSEYGLDK--VVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64
           +++L PY PGKP++ +  E  LD   +VKLASNENP G S    +A+  E+ +L  YPDG
Sbjct: 13  VQKLSPYVPGKPVDELARELNLDPAGIVKLASNENPLGPSPKVLDAIRAELSELTRYPDG 72

Query: 65  YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124
              AL+ RL++  +V    +  GNGS++I+++I RA+L    N V +   F  Y      
Sbjct: 73  NGFALKQRLAERYSVGINQVTLGNGSNDILELIARAYLAPGLNAVFSEHAFAVYPIATQA 132

Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184
            GAE R +  +  G HDLDAM  AIDE T+VV++ +PNNPTGT+     L  FL RVP  
Sbjct: 133 VGAEGRAVPAKNWG-HDLDAMAAAIDENTRVVFVANPNNPTGTWFDAAALGGFLARVPEH 191

Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244
           VLVVLDEAY EY   ++ P+ +  L+ Y NL++ RTFSKAYGLAALRVGY I+   +   
Sbjct: 192 VLVVLDEAYIEYAEGQELPDGLAFLADYPNLLVSRTFSKAYGLAALRVGYAISSPVIADV 251

Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304
           +   R+PFN + L  AAA AALDD  ++ +  + N+AG+ Q     +  GL+  PS+ NF
Sbjct: 252 LNRVRQPFNVNSLALAAACAALDDVDYLLASRKANDAGMLQLETGFRQLGLEWIPSRGNF 311

Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
           + +DF R A  + QALL +G IVR     G PT LR++IGT+++N   L +L ++L
Sbjct: 312 IAVDFARDATPINQALLREGVIVRPVAGYGMPTFLRVSIGTEQENARFLDVLRQVL 367


Lambda     K      H
   0.317    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: 358
Number of extensions: 18
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: 360
Length of database: 369
Length adjustment: 29
Effective length of query: 331
Effective length of database: 340
Effective search space:   112540
Effective search space used:   112540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate GFF1942 Psest_1985 (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.23542.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.2e-118  379.6   0.0     7e-118  379.4   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1942  Psest_1985 histidinol-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1942  Psest_1985 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.4   0.0    7e-118    7e-118       2     349 .]      11     366 ..      10     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.4 bits;  conditional E-value: 7e-118
                           TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakyl 68 
                                         + ++kl+pY+pg      arel  +  ++vkL+snEnP+gps+kv++a+++el++l+rYpd ++++lk++la+++
  lcl|FitnessBrowser__psRCH2:GFF1942  11 PGVQKLSPYVPGkpvdelARELNLDpaGIVKLASNENPLGPSPKVLDAIRAELSELTRYPDGNGFALKQRLAERY 85 
                                         679***************999999999************************************************ PP

                           TIGR01141  69 gveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakek 143
                                         +v+ ++++lgnGs++++el++ra+l pg +++++e+++++Y++ +++ gae + vp+k++g +dl+a+++a++e+
  lcl|FitnessBrowser__psRCH2:GFF1942  86 SVGINQVTLGNGSNDILELIARAYLAPGLNAVFSEHAFAVYPIATQAVGAEGRAVPAKNWG-HDLDAMAAAIDEN 159
                                         *********************************************************9995.9************ PP

                           TIGR01141 144 vklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgL 214
                                         +++vf+a+PnnPtG++++++ +  +l++v e++lVV+DeAYie++e    ++ l +la+ypnl+v+rT+SKa+gL
  lcl|FitnessBrowser__psRCH2:GFF1942 160 TRVVFVANPNNPTGTWFDAAALGGFLARVpEHVLVVLDEAYIEYAEGqelPDGLAFLADYPNLLVSRTFSKAYGL 234
                                         *****************************99**************99899999********************** PP

                           TIGR01141 215 AglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSk 289
                                         A+lRvGyai+++ i+++l++vr+p+nv+slal+aa+aal+d d++ ++ +++ +++ +l++++++l gle+++S 
  lcl|FitnessBrowser__psRCH2:GFF1942 235 AALRVGYAISSPVIADVLNRVRQPFNVNSLALAAACAALDDVDYLLASRKANDAGMLQLETGFRQL-GLEWIPSR 308
                                         ******************************************************************.8******* PP

                           TIGR01141 290 aNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349
                                         +NF+ +++ +da+ + +all++g+ivR ++ + g+ +++lR+++Gt++en r+l++l+++
  lcl|FitnessBrowser__psRCH2:GFF1942 309 GNFIAVDFARDATPINQALLREGVIVRPVAGY-GM-PTFLRVSIGTEQENARFLDVLRQV 366
                                         ********************************.96.*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (369 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: 6.99
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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