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.3283006.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.16
//
[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:

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