Alignments for a candidate for hisC in Pseudomonas stutzeri RCH2

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.9137.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: 7.36
//
[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