Alignments for a candidate for hisC in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Pseudomonas fluorescens FW300-N2E2

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate Pf6N2E2_3251 Histidinol-phosphate aminotransferase (EC 2.6.1.9)

Query= reanno::pseudo6_N2E2:Pf6N2E2_3251
         (350 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251
          Length = 350

 Score =  704 bits (1818), Expect = 0.0
 Identities = 350/350 (100%), Positives = 350/350 (100%)

Query: 1   MSKFWSPFVKNLVPYVPGEQPKLTRLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60
           MSKFWSPFVKNLVPYVPGEQPKLTRLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP
Sbjct: 1   MSKFWSPFVKNLVPYVPGEQPKLTRLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60

Query: 61  NSDLLKGAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120
           NSDLLKGAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL
Sbjct: 61  NSDLLKGAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120

Query: 121 YGIQFDAVPLDAQFQIDPADYAKPNGGIIFPNPNAPTGCLLALEAVEQILKANPDSVVVV 180
           YGIQFDAVPLDAQFQIDPADYAKPNGGIIFPNPNAPTGCLLALEAVEQILKANPDSVVVV
Sbjct: 121 YGIQFDAVPLDAQFQIDPADYAKPNGGIIFPNPNAPTGCLLALEAVEQILKANPDSVVVV 180

Query: 181 DEAYIDFGGETAISLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFN 240
           DEAYIDFGGETAISLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFN
Sbjct: 181 DEAYIDFGGETAISLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFN 240

Query: 241 SYPLDRLANVGGAAAFDDREYFDRTCRLVIEHREWVVAQLQAKGFEVLPSAANFIFARHP 300
           SYPLDRLANVGGAAAFDDREYFDRTCRLVIEHREWVVAQLQAKGFEVLPSAANFIFARHP
Sbjct: 241 SYPLDRLANVGGAAAFDDREYFDRTCRLVIEHREWVVAQLQAKGFEVLPSAANFIFARHP 300

Query: 301 RHDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIEALGEL 350
           RHDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIEALGEL
Sbjct: 301 RHDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIEALGEL 350


Lambda     K      H
   0.320    0.139    0.413 

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: 648
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: 350
Length of database: 350
Length adjustment: 29
Effective length of query: 321
Effective length of database: 321
Effective search space:   103041
Effective search space used:   103041
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 Pf6N2E2_3251 (Histidinol-phosphate aminotransferase (EC 2.6.1.9))
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.5354.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    4.5e-97  311.0   0.0    5.1e-97  310.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251  Histidinol-phosphate aminotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251  Histidinol-phosphate aminotransferase (EC 2.6.1.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.8   0.0   5.1e-97   5.1e-97       3     348 ..       8     349 ..       6     350 .] 0.95

  Alignments for each domain:
  == domain 1  score: 310.8 bits;  conditional E-value: 5.1e-97
                                      TIGR01141   3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkeala 65 
                                                     +k+l pY+pg++ + +   vkLn+nEnP+gps+k+++a++ el+ +l++Ypdp++  lk a+a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251   8 FVKNLVPYVPGEQPKLT-RLVKLNTNENPYGPSPKALAAMQTELNdNLRLYPDPNSDLLKGAVA 70 
                                                    699*******9777777.6*************************99****************** PP

                                      TIGR01141  66 kylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedg 129
                                                    +y+gv+ ++++lgnGsde++  +++ +l+  +  l+++ +ys Y+v+  ++g++   vpl++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251  71 RYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGLYGIQFDAVPLDAQF 134
                                                    ***************************************************************9 PP

                                      TIGR01141 130 qedleavleaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvl 193
                                                    q d ++ +   k +  ++f  +Pn+PtG ll  e +e++l++  d +VVvDeAYi+F +e +++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251 135 QIDPADYA---KPNGGIIF-PNPNAPTGCLLALEAVEQILKANPDSVVVVDEAYIDFGGE-TAI 193
                                                    99988888...55555665.89********************77***************7.*** PP

                                      TIGR01141 194 ellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalr 254
                                                    +l+ +ypnl+v++TlSK+ +LAglRvG+a++++e+ieale++++++n   +++la   + aa +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251 194 SLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFNsypLDRLANVGGAAAFD 257
                                                    *******************************************87543339************* PP

                                      TIGR01141 255 dsdkiektveevkkererlleelkkleglevyeSkaNFvlikvke.daeelleallekgiivRd 317
                                                    d++++ +t + v+++re++ ++l++  g+ev +S aNF++++ ++ da+ l+ +l e+g+ivR+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251 258 DREYFDRTCRLVIEHREWVVAQLQAK-GFEVLPSAANFIFARHPRhDAAGLAAKLREQGVIVRH 320
                                                    ************************87.9****************99****************** PP

                                      TIGR01141 318 lksaeglleeclRitvGtreenerllealke 348
                                                    +k+    + ++lRi++Gt+e+n++l+eal e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3251 321 FKQE--RIAQFLRISIGTPEQNQALIEALGE 349
                                                    *977..48********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (350 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.91
//
[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