GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisC in Pseudomonas fluorescens FW300-N2C3

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate AO356_03460 AO356_03460 aspartate aminotransferase

Query= curated2:Q9RI00
         (366 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460 AO356_03460
           aspartate aminotransferase
          Length = 370

 Score =  443 bits (1140), Expect = e-129
 Identities = 236/371 (63%), Positives = 277/371 (74%), Gaps = 11/371 (2%)

Query: 1   MSADFLALAVPGVQKLSPYVTGKPIDELARELGIEPARIVKLASNENPLGPNPRVLEAVR 60
           MS +FLALA PGVQ+LSPYV GKP+DELAREL ++PA IVKLASNENPLG +P+ L A+R
Sbjct: 1   MSGNFLALAQPGVQQLSPYVPGKPVDELARELDLDPASIVKLASNENPLGASPKALAAIR 60

Query: 61  GELSELTRYPDGSGFRLKAKLAERFGLKSEQITLGNGSNDIIDLVARC-CGAGPNAVFSA 119
            EL+ELTRYPDG+GF LK+ LAER G++  Q+TLGNGSNDI++LVAR     G NAVFS 
Sbjct: 61  DELAELTRYPDGNGFALKSLLAERCGVELNQVTLGNGSNDILELVARAYLAPGLNAVFSE 120

Query: 120 HAFAAYPLCTQAAGAESRVVPAVDYGHDLDGMLKAIDEQTAVIFIANPNNPTGNLVRAQA 179
           HAFA YP+ TQA GA++ VVPA D+GHDL  ML AID  T V+FIANPNNPTG    AQA
Sbjct: 121 HAFAVYPIATQAVGADAHVVPAKDWGHDLPAMLAAIDANTRVVFIANPNNPTGTWFDAQA 180

Query: 180 LESFLDRVPERVLVVLDEAYIEFYRGTNC-QRLNYLVRYPNLLVSRTLSKVYGLAGLRVG 238
           L+ FL  VP  VLVVLDEAYIE+  G++    L++L  YPNLLVSRT SK YGLA LRVG
Sbjct: 181 LDDFLQDVPAHVLVVLDEAYIEYAEGSDLPDGLDFLAAYPNLLVSRTFSKAYGLASLRVG 240

Query: 239 YSASSPQIADVLNRVRQPFNVNSLALVAACA-----GWMTSSIWLKGGGWIAPVWELEQG 293
           Y  S+  +ADVLNRVRQPFNVNS AL AACA      ++  S  L   G    + +LE G
Sbjct: 241 YGLSTAVVADVLNRVRQPFNVNSFALAAACAALQDEAYLAESRRLNAAG----MQQLEAG 296

Query: 294 LAELRLKWIPSRGNFLAVDLGRDAAPINAGLLRDGVIVRPIAGYDCPTFLRVSIGTEQEN 353
           L EL L WIPS+GNF+ VDLGR AAP+  GLLR+GVIVRP+A Y  P  LR++IG   EN
Sbjct: 297 LRELGLGWIPSKGNFICVDLGRVAAPVYQGLLREGVIVRPVANYGMPNHLRITIGLPTEN 356

Query: 354 ARFLEALRVVL 364
           +RFLEAL  VL
Sbjct: 357 SRFLEALSKVL 367


Lambda     K      H
   0.320    0.138    0.412 

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: 476
Number of extensions: 22
Number of successful extensions: 4
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: 366
Length of database: 370
Length adjustment: 30
Effective length of query: 336
Effective length of database: 340
Effective search space:   114240
Effective search space used:   114240
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 AO356_03460 AO356_03460 (aspartate 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.13670.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     1e-115  372.3   0.0   1.1e-115  372.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460  AO356_03460 aspartate aminotrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460  AO356_03460 aspartate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.2   0.0  1.1e-115  1.1e-115       2     348 ..      11     365 ..      10     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 1.1e-115
                                       TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpq 56 
                                                     + +++l+pY+pg      arel  +   +vkL+snEnP+g s+k+++a+++el++l+rYpd +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460  11 PGVQQLSPYVPGkpvdelARELDLDpaSIVKLASNENPLGASPKALAAIRDELAELTRYPDGN 73 
                                                     679***************999999999************************************ PP

                                       TIGR01141  57 alelkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagae 119
                                                     +++lk+ la+++gve ++++lgnGs++++el++ra+l pg +++++e+++++Y++ +++ ga+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460  74 GFALKSLLAERCGVELNQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQAVGAD 136
                                                     *************************************************************** PP

                                       TIGR01141 120 vkevplkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDe 181
                                                        vp+k++g +dl+a+l+a++ ++++vf+a+PnnPtG++++++ + ++l+ v +++lVV+De
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460 137 AHVVPAKDWG-HDLPAMLAAIDANTRVVFIANPNNPTGTWFDAQALDDFLQDVpAHVLVVLDE 198
                                                     *****99995.9*****************************************88******** PP

                                       TIGR01141 182 AYieFsee...asvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynv 241
                                                     AYie++e    ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++a ++++l++vr+p+nv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460 199 AYIEYAEGsdlPDGLDFLAAYPNLLVSRTFSKAYGLASLRVGYGLSTAVVADVLNRVRQPFNV 261
                                                     ******999999*************************************************** PP

                                       TIGR01141 242 sslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvkedaeel 304
                                                     +s al+aa+aal+d+++++++ + +++++++l+++l++l gl +++Sk+NF+ +++ + a+ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460 262 NSFALAAACAALQDEAYLAESRRLNAAGMQQLEAGLREL-GLGWIPSKGNFICVDLGRVAAPV 323
                                                     ***************************************.8********************** PP

                                       TIGR01141 305 leallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                                     ++ ll++g+ivR ++++ g+ +++lRit+G + en r+leal++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460 324 YQGLLREGVIVRPVANY-GM-PNHLRITIGLPTENSRFLEALSK 365
                                                     *****************.96.********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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: 9.87
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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