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 (EC 2.6.1.9) (characterized)
to candidate GFF3234 Psest_3297 histidinol-phosphate aminotransferase

Query= reanno::psRCH2:GFF3234
         (348 letters)



>FitnessBrowser__psRCH2:GFF3234
          Length = 348

 Score =  692 bits (1786), Expect = 0.0
 Identities = 348/348 (100%), Positives = 348/348 (100%)

Query: 1   MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP 60
           MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP
Sbjct: 1   MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP 60

Query: 61  NGERLKQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGL 120
           NGERLKQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGL
Sbjct: 61  NGERLKQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGL 120

Query: 121 YGIAYETVALDEQFQIDVADYNRPNGGIIFPNPNAPTGCLLALEAIERLLQANTETVVLV 180
           YGIAYETVALDEQFQIDVADYNRPNGGIIFPNPNAPTGCLLALEAIERLLQANTETVVLV
Sbjct: 121 YGIAYETVALDEQFQIDVADYNRPNGGIIFPNPNAPTGCLLALEAIERLLQANTETVVLV 180

Query: 181 DEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN 240
           DEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN
Sbjct: 181 DEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN 240

Query: 241 SYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIFARHP 300
           SYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIFARHP
Sbjct: 241 SYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIFARHP 300

Query: 301 QRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEALG 348
           QRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEALG
Sbjct: 301 QRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEALG 348


Lambda     K      H
   0.320    0.137    0.401 

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: 630
Number of extensions: 19
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: 348
Length of database: 348
Length adjustment: 29
Effective length of query: 319
Effective length of database: 319
Effective search space:   101761
Effective search space used:   101761
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: 49 (23.5 bits)

Align candidate GFF3234 Psest_3297 (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.5993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      6e-97  310.6   0.0    6.8e-97  310.4   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3234  Psest_3297 histidinol-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3234  Psest_3297 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.4   0.0   6.8e-97   6.8e-97       3     346 ..       8     347 ..       6     348 .] 0.94

  Alignments for each domain:
  == domain 1  score: 310.4 bits;  conditional E-value: 6.8e-97
                           TIGR01141   3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylgveeenil 76 
                                          +k+l pY+pg++ +   + vkLn+nEnP+gps+++++a+++el+ +l++Ypdp++ +lk+a+a+y+gv++++++
  lcl|FitnessBrowser__psRCH2:GFF3234   8 FVKDLVPYVPGEQPKLS-KLVKLNTNENPYGPSPRAIAAMQAELNdSLRLYPDPNGERLKQAVADYYGVQPAQVF 81 
                                         699*******9766666.6*************************999**************************** PP

                           TIGR01141  77 lgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflas 151
                                         +gnGsde++   ++ + +     l+++ +ys Y+v+  ++g+ + +v+l+e++q d+++ +     +  ++ + +
  lcl|FitnessBrowser__psRCH2:GFF3234  82 VGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGLYGIAYETVALDEQFQIDVADYN---RPNGGII-FPN 152
                                         ****************************************************988888777...4444555.58* PP

                           TIGR01141 152 PnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaiana 226
                                         Pn+PtG ll  e ie++l++ ++++V+vDeAY++F +e s++ l+ +ypnl+v++TlSK+ +LAglRvG+a++++
  lcl|FitnessBrowser__psRCH2:GFF3234 153 PNAPTGCLLALEAIERLLQANTETVVLVDEAYVDFGGE-SAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHP 226
                                         ********************889**************7.************************************ PP

                           TIGR01141 227 eiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvk 298
                                         ++ieale++++++n   ++++a + a aa +d++++++t ++v+ +re + ++++ l g+ev +S aNF++++ +
  lcl|FitnessBrowser__psRCH2:GFF3234 227 DLIEALERIKNSFNsypLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGL-GFEVLPSAANFIFARHP 300
                                         **********87543339***************************************.8***************9 PP

                           TIGR01141 299 e.daeelleallekgiivRdlksaeglleeclRitvGtreenerlleal 346
                                         + da+ ++ +l e+g+ivR++k+    +e++lRit+Gt+e+n++lleal
  lcl|FitnessBrowser__psRCH2:GFF3234 301 QrDAATIAASLREQGVIVRHFKQR--RIEQFLRITIGTPEQNQALLEAL 347
                                         99*******************977..58*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (348 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: 6.63
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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