Alignments for a candidate for trpE in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Dechlorosoma suillum PS

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate Dsui_0219 Dsui_0219 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__PS:Dsui_0219
          Length = 491

 Score =  571 bits (1471), Expect = e-167
 Identities = 296/488 (60%), Positives = 364/488 (74%), Gaps = 5/488 (1%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M   EF  LAA GYNRIP+  ET AD DTPLSIYLKLA+ P +YLLESVQGGE++GRYS+
Sbjct: 1   MTETEFNALAAQGYNRIPVTLETFADLDTPLSIYLKLANGPYTYLLESVQGGERFGRYSI 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGL S T + V+G+ V +L      E  +  +PL F+ES++ R++VA   GLPRF GGLV
Sbjct: 61  IGLASPTRIAVYGHQVMVLTGQRIAERENDTNPLEFIESYQKRFRVAPYAGLPRFCGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           G FGYD VRYVE RL  S   D LG PDILL++S+ + V DNL+GK+  +V  +P    A
Sbjct: 121 GCFGYDTVRYVETRLTKSAKHDELGTPDILLLLSEEIAVVDNLSGKLTLVVYAEPGFPGA 180

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           F++ +ARL+ LL  LR P      +    P  ++P   S +    ++ AV + KEYI  G
Sbjct: 181 FQKARARLKELLAQLRTPAP----IPEEKPATSQPAV-SIFGEAPFKQAVAKAKEYITEG 235

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           D MQVV SQRM+  F A+P+ LYRALR  NP+PYMY+F+F DFHVVG+SPE+L R+E + 
Sbjct: 236 DIMQVVLSQRMTKPFSASPLSLYRALRTLNPSPYMYYFDFEDFHVVGASPEILTRLEGDT 295

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           VTVRPIAGTR RGAT E D AL +DLL+D KEIAEH+ L+DLGRNDVGRV+ TGSV+LTE
Sbjct: 296 VTVRPIAGTRKRGATPEEDAALAEDLLADQKEIAEHVQLLDLGRNDVGRVAQTGSVKLTE 355

Query: 361 KMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           +M IERYS+VMHIVSNV G+L+ GL+A+D L+A  PAGTLSGAPK+RAMEIIDELEPVKR
Sbjct: 356 RMSIERYSHVMHIVSNVEGKLQAGLSALDVLKAAFPAGTLSGAPKVRAMEIIDELEPVKR 415

Query: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           G+YGGA+GY  +NG+MD AIAIRTAVI DG+LHVQAG GIVADS P  EW+ET NK RA+
Sbjct: 416 GIYGGAIGYLGFNGDMDLAIAIRTAVIKDGQLHVQAGAGIVADSDPTSEWQETQNKARAV 475

Query: 481 FRAVALAE 488
            RA  +AE
Sbjct: 476 LRAAEMAE 483


Lambda     K      H
   0.320    0.138    0.403 

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: 703
Number of extensions: 24
Number of successful extensions: 2
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: 493
Length of database: 491
Length adjustment: 34
Effective length of query: 459
Effective length of database: 457
Effective search space:   209763
Effective search space used:   209763
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: 52 (24.6 bits)

Align candidate Dsui_0219 Dsui_0219 (anthranilate synthase component I)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))

# 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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.2828.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: anthranilate synthase component I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-176  573.9   0.0   1.6e-176  573.7   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0219  Dsui_0219 anthranilate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0219  Dsui_0219 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.7   0.0  1.6e-176  1.6e-176       2     454 ..      26     479 ..      25     480 .. 0.94

  Alignments for each domain:
  == domain 1  score: 573.7 bits;  conditional E-value: 1.6e-176
                         TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelrklle 77 
                                       d  tp+s+ylkla+ ++++llEsv+ +e+ gRyS+igl + ++i++ +++++ l+ +  +++ +++++l+ +++  +
  lcl|FitnessBrowser__PS:Dsui_0219  26 DLDTPLSIYLKLANGPYTYLLESVQGGERFGRYSIIGLASPTRIAVYGHQVMVLTGQRIAEReNDTNPLEFIESYQK 102
                                       778**********99*************************************999888777768999********** PP

                         TIGR00564  78 ka.eesedeldeplsggavGylgydtvrlveklke.ea.edelelpdlllllvetvivfDhvekkvilienarteae 151
                                       ++      +l+  ++gg+vG +gydtvr+ve+  + +a +del +pd+llll e+++v D+ + k++l+ +a+    
  lcl|FitnessBrowser__PS:Dsui_0219 103 RFrVAPYAGLPR-FCGGLVGCFGYDTVRYVETRLTkSAkHDELGTPDILLLLSEEIAVVDNLSGKLTLVVYAEPGFP 178
                                       *94444555655.******************865534459*******************************977665 PP

                         TIGR00564 152 rsaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveak 228
                                         a+++a+arl+ella+l++++    + ++ ++++  s + ++ ++++vakakeyi++Gdi+qvvlSqr++++++a+
  lcl|FitnessBrowser__PS:Dsui_0219 179 G-AFQKARARLKELLAQLRTPAPIPEE-KPATSQPAVSIFGEAPFKQAVAKAKEYITEGDIMQVVLSQRMTKPFSAS 253
                                       5.9******************974333.33334446688899*********************************** PP

                         TIGR00564 229 pfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAE 305
                                       p++lYr+LRt NPSpy+yy+d+edf++vg+SPE+l +++g++v++rPiAGtrkRGat+eeD+al+e+Llad+Ke AE
  lcl|FitnessBrowser__PS:Dsui_0219 254 PLSLYRALRTLNPSPYMYYFDFEDFHVVGASPEILTRLEGDTVTVRPIAGTRKRGATPEEDAALAEDLLADQKEIAE 330
                                       ***************************************************************************** PP

                         TIGR00564 306 HlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmeli 382
                                       H+ L+DL+RND+g+va++gsv+ +e ++ie+yshvmHivS+VeG+l+ +l+a+D+l+aa+PaGTlsGAPKvrAme+i
  lcl|FitnessBrowser__PS:Dsui_0219 331 HVQLLDLGRNDVGRVAQTGSVKLTERMSIERYSHVMHIVSNVEGKLQAGLSALDVLKAAFPAGTLSGAPKVRAMEII 407
                                       ***************************************************************************** PP

                         TIGR00564 383 delEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                       delE++kRgiYgGa+gyl+f+gd+d aiaiRt+v+kdg+++vqAgaGiVaDSdp++E++Et nKa+a+lra+
  lcl|FitnessBrowser__PS:Dsui_0219 408 DELEPVKRGIYGGAIGYLGFNGDMDLAIAIRTAVIKDGQLHVQAGAGIVADSDPTSEWQETQNKARAVLRAA 479
                                       *********************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (491 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: 00:00:00.02
# Mc/sec: 11.10
//
[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:

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, 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

GapMind for Amino acid biosynthesis