GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Pedobacter sp. GW460-11-11-14-LB5

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate CA265_RS05025 CA265_RS05025 tryptophan synthase subunit alpha

Query= uniprot:A0A3N7DTH5
         (255 letters)



>FitnessBrowser__Pedo557:CA265_RS05025
          Length = 255

 Score =  404 bits (1037), Expect = e-117
 Identities = 196/254 (77%), Positives = 222/254 (87%)

Query: 1   MNRINKLFQEKKNILSIYYTAGYPNLGDTVAIAEELERSGADLLEIGFPYSDPVADGPVI 60
           MNRI +LFQEKKNILSIYYTAGYPN GDT+ IAE LE+SGAD+LEIGFPYSDPVADGPVI
Sbjct: 1   MNRIKQLFQEKKNILSIYYTAGYPNTGDTLQIAEALEQSGADMLEIGFPYSDPVADGPVI 60

Query: 61  QASSKTALDGGMTLKLLFEQLKDLRKTVNIPVLLMGYVNPMLQYGVENFCKSCAEVGVDG 120
           QASSK +LD GMTL+LLFEQLKDLRK V IPVLLMGYVNP+LQ+GVE FC++CAEVGVDG
Sbjct: 61  QASSKQSLDQGMTLQLLFEQLKDLRKKVTIPVLLMGYVNPVLQFGVEKFCEACAEVGVDG 120

Query: 121 CIVPDLPMVEYEELYSGVFEANGLTNIFLVTPQTSTERIRKIDGLSNGFIYLLSSSATTG 180
           CIVPDLPMVEYEE Y   FE + L+N+FL+TPQT+ ERI KIDGL+NGFIYLLSSSATTG
Sbjct: 121 CIVPDLPMVEYEEFYKDCFEKHNLSNVFLITPQTAEERIHKIDGLTNGFIYLLSSSATTG 180

Query: 181 QNLQVSENTEAYFSRIAEMKLNNPTMIGFGISSKETFDKACQYANGAIIGSAFVKSLKSG 240
           +NL+V   TEAYFSRI  + L NPTMIGFGIS K+TFDKAC YANGAIIG+AFVK++  G
Sbjct: 181 KNLEVGNTTEAYFSRIKNLNLKNPTMIGFGISDKQTFDKACSYANGAIIGTAFVKAIADG 240

Query: 241 KVTDSVKDFMKTFK 254
            + +SV +FMK FK
Sbjct: 241 NLAESVSNFMKKFK 254


Lambda     K      H
   0.317    0.135    0.382 

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: 320
Number of extensions: 8
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate CA265_RS05025 CA265_RS05025 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

# 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.1552.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
      9e-73  230.3   0.0      1e-72  230.1   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS05025  CA265_RS05025 tryptophan synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS05025  CA265_RS05025 tryptophan synthase subunit alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1   0.0     1e-72     1e-72       3     239 ..       6     241 ..       4     255 .] 0.94

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 1e-72
                                  TIGR00262   3 tlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvk 70 
                                                +l +++++ +  ++tag+P++  +l+i++ l ++Gad+lE+G+p+sDP+aDGp+iqa+++  l++g++
  lcl|FitnessBrowser__Pedo557:CA265_RS05025   6 QLFQEKKNILSIYYTAGYPNTGDTLQIAEALEQSGADMLEIGFPYSDPVADGPVIQASSKQSLDQGMT 73 
                                                667788889999******************************************************** PP

                                  TIGR00262  71 vekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaa.k 137
                                                ++  +e lk +r+k ++iP+ l+ y n++++ gve+F + ++e+gvdg +v+DlP+ e +++++ + +
  lcl|FitnessBrowser__Pedo557:CA265_RS05025  74 LQLLFEQLKDLRKK-VTIPVLLMGYVNPVLQFGVEKFCEACAEVGVDGCIVPDLPMVEYEEFYKDCfE 140
                                                **************.*************************************************9978 PP

                                  TIGR00262 138 khgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkals.kkPvlvG 204
                                                kh+++++fl++P++ eer++ki+  ++Gf+Yl+s++  tg + +v +++++   ++k+l+ k P ++G
  lcl|FitnessBrowser__Pedo557:CA265_RS05025 141 KHNLSNVFLITPQTAEERIHKIDGLTNGFIYLLSSSATTGKNLEVGNTTEAYFSRIKNLNlKNPTMIG 208
                                                9*********************************************************98578***** PP

                                  TIGR00262 205 FGiskkeqvkelkelgadgvivGsAlvkiieekld 239
                                                FGis k+   ++ +  a+g+i+G A+vk i++  +
  lcl|FitnessBrowser__Pedo557:CA265_RS05025 209 FGISDKQTFDKACSY-ANGAIIGTAFVKAIADG-N 241
                                                **************9.899***********986.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (255 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: 00:00:00.00
# Mc/sec: 6.96
//
[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