GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Pseudomonas fluorescens GW456-L13

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate PfGW456L13_4999 Histidinol-phosphate aminotransferase (EC 2.6.1.9)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999
          Length = 350

 Score =  665 bits (1716), Expect = 0.0
 Identities = 328/350 (93%), Positives = 343/350 (98%)

Query: 1   MSKFWSPFVKNLVPYVPGEQPKLTRLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60
           MSKFWSPFVKNLVPYVPGEQPKL +LVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP
Sbjct: 1   MSKFWSPFVKNLVPYVPGEQPKLAKLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60

Query: 61  NSDLLKGAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120
           NSDLLK AVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL
Sbjct: 61  NSDLLKNAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120

Query: 121 YGIQFDAVPLDAQFQIDPADYAKPNGGIIFPNPNAPTGCLLALEAVEQILKANPDSVVVV 180
           YGI+FDAVPLD QFQI+PADYA+PNGGIIFPNPNAPTGCLLALEAVEQILKA+PDSVVVV
Sbjct: 121 YGIKFDAVPLDEQFQINPADYARPNGGIIFPNPNAPTGCLLALEAVEQILKASPDSVVVV 180

Query: 181 DEAYIDFGGETAISLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFN 240
           DEAYIDFGGETAI+LVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHP+LIEALERIKNSFN
Sbjct: 181 DEAYIDFGGETAITLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN 240

Query: 241 SYPLDRLANVGGAAAFDDREYFDRTCRLVIEHREWVVAQLQAKGFEVLPSAANFIFARHP 300
           SYPLDR+ANVG AAAF+DREYFD+TCRLVIE+RE VVAQL+ KGFEVLPSAANFIFARHP
Sbjct: 241 SYPLDRMANVGAAAAFEDREYFDKTCRLVIENREKVVAQLEEKGFEVLPSAANFIFARHP 300

Query: 301 RHDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIEALGEL 350
           R+DAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALI+ LG+L
Sbjct: 301 RYDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIDGLGDL 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: 614
Number of extensions: 12
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 PfGW456L13_4999 (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.7495.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    3.8e-96  307.9   0.0    4.3e-96  307.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999  Histidinol-phosphate aminotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999  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 !  307.8   0.0   4.3e-96   4.3e-96       3     347 ..       8     348 ..       6     350 .] 0.94

  Alignments for each domain:
  == domain 1  score: 307.8 bits;  conditional E-value: 4.3e-96
                                               TIGR01141   3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpq 56 
                                                              +k+l pY+pg++ +   + vkLn+nEnP+gps+k+++a++ el+ +l++Ypdp+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999   8 FVKNLVPYVPGEQPKLA-KLVKLNTNENPYGPSPKALAAMQTELNdNLRLYPDPN 61 
                                                             699*******9777766.5*************************99********* PP

                                               TIGR01141  57 alelkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYev 111
                                                             +  lk+a+a+y+gv+ ++++lgnGsde++  +++ +l+  +  l+++ +ys Y+v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999  62 SDLLKNAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPV 116
                                                             ******************************************************* PP

                                               TIGR01141 112 sakiagaevkevplkedgqedleavleaakekvklvflasPnnPtGnllkreeie 166
                                                             +  ++g++   vpl+e++q + ++ +     +   + + +Pn+PtG ll  e +e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 117 YCGLYGIKFDAVPLDEQFQINPADYA---RPNGG-IIFPNPNAPTGCLLALEAVE 167
                                                             *****************988888877...44444.5558**************** PP

                                               TIGR01141 167 kvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGy 221
                                                             ++l+++ d +VVvDeAYi+F +e +++ l+ +ypnl+v++TlSK+ +LAglRvG+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 168 QILKASPDSVVVVDEAYIDFGGE-TAITLVDRYPNLLVTQTLSKSRSLAGLRVGL 221
                                                             *****98***************7.******************************* PP

                                               TIGR01141 222 aianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererl 273
                                                             a++++++ieale++++++n   ++++a   a aa +d++++ kt + v+++re +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 222 AVGHPDLIEALERIKNSFNsypLDRMANVGAAAAFEDREYFDKTCRLVIENREKV 276
                                                             ***************875433399******************************* PP

                                               TIGR01141 274 leelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaegllee 327
                                                              ++l++  g+ev +S aNF++++ ++ da+ l+ +l e+g+ivR++k+    + +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 277 VAQLEEK-GFEVLPSAANFIFARHPRyDAAGLAAKLREQGVIVRHFKQE--RIAQ 328
                                                             *****99.8****************99*******************977..48** PP

                                               TIGR01141 328 clRitvGtreenerllealk 347
                                                             +lRi++Gt+e+n++l++ l 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 329 FLRISIGTPEQNQALIDGLG 348
                                                             ***************98775 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.79
//
[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