Alignments for a candidate for hisC in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Pseudomonas fluorescens FW300-N1B4

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate Pf1N1B4_1065 Histidinol-phosphate aminotransferase (EC 2.6.1.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065
          Length = 350

 Score =  656 bits (1692), Expect = 0.0
 Identities = 324/350 (92%), Positives = 340/350 (97%)

Query: 1   MSKFWSPFVKNLVPYVPGEQPKLTRLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60
           MSKFWSPFVK+LVPYVPGEQPKL +LVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP
Sbjct: 1   MSKFWSPFVKSLVPYVPGEQPKLAKLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60

Query: 61  NSDLLKGAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120
           NSDLLK AVA+YYGVQ NQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL
Sbjct: 61  NSDLLKQAVAKYYGVQGNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120

Query: 121 YGIQFDAVPLDAQFQIDPADYAKPNGGIIFPNPNAPTGCLLALEAVEQILKANPDSVVVV 180
           YGI FDAVPLD QFQI+PADYAKPNGGIIFPNPNAPTGCLLAL+AVEQILKA+PDSVVVV
Sbjct: 121 YGIAFDAVPLDEQFQINPADYAKPNGGIIFPNPNAPTGCLLALDAVEQILKASPDSVVVV 180

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

Query: 241 SYPLDRLANVGGAAAFDDREYFDRTCRLVIEHREWVVAQLQAKGFEVLPSAANFIFARHP 300
           SYPLDRLA VG AAAF+DREYFD+TCRLVI+ RE VVAQL+AKGFEVLPSAANFIFARHP
Sbjct: 241 SYPLDRLAIVGAAAAFEDREYFDKTCRLVIDSREKVVAQLEAKGFEVLPSAANFIFARHP 300

Query: 301 RHDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIEALGEL 350
           +HDAAGLAAKLRE+GVIVRHFKQERIAQFLRISIGTPEQNQALI+ LG+L
Sbjct: 301 KHDAAGLAAKLRERGVIVRHFKQERIAQFLRISIGTPEQNQALIDGLGDL 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: 600
Number of extensions: 14
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 Pf1N1B4_1065 (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.668387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
      2e-95  305.6   0.0    2.2e-95  305.4   0.0    1.0  1  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.4   0.0   2.2e-95   2.2e-95       3     347 ..       8     348 ..       6     350 .] 0.94

  Alignments for each domain:
  == domain 1  score: 305.4 bits;  conditional E-value: 2.2e-95
                                  TIGR01141   3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylg 69 
                                                 +k+l pY+pg++ +   + vkLn+nEnP+gps+k+++a++ el+ +l++Ypdp++  lk+a+aky+g
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065   8 FVKSLVPYVPGEQPKLA-KLVKLNTNENPYGPSPKALAAMQTELNdNLRLYPDPNSDLLKQAVAKYYG 74 
                                                699*******9777766.5*************************99********************** PP

                                  TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavl 137
                                                v+ ++++lgnGsde++  +++ +l+  +  l+++ +ys Y+v+  ++g+    vpl+e++q + ++ +
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065  75 VQGNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGLYGIAFDAVPLDEQFQINPADYA 142
                                                ***********************************************************988888887 PP

                                  TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvl 205
                                                   k +  ++f  +Pn+PtG ll  + +e++l+++ d +VVvDeAYi+F +e +++ l+ +ypnl+v+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065 143 ---KPNGGIIF-PNPNAPTGCLLALDAVEQILKASPDSVVVVDEAYIDFGGE-TAITLVDRYPNLLVT 205
                                                ...55555555.89********************98***************7.*************** PP

                                  TIGR01141 206 rTlSKafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkker 270
                                                +TlSK+ +LAglRvG+a++++++ieale++++++n   +++la   a aa +d++++ kt + v+ +r
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065 206 QTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFNsypLDRLAIVGAAAAFEDREYFDKTCRLVIDSR 273
                                                *******************************87543339***************************** PP

                                  TIGR01141 271 erlleelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtre 337
                                                e + ++l++  g+ev +S aNF++++ ++ da+ l+ +l e+g+ivR++k+    + ++lRi++Gt+e
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065 274 EKVVAQLEAK-GFEVLPSAANFIFARHPKhDAAGLAAKLRERGVIVRHFKQE--RIAQFLRISIGTPE 338
                                                ********87.9***************999*******************977..48************ PP

                                  TIGR01141 338 enerllealk 347
                                                +n++l++ l 
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065 339 QNQALIDGLG 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: 00:00:00.00
# Mc/sec: 23.04
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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