Alignments for a candidate for trpE in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Geobacter lovleyi SZ

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_012470593.1 GLOV_RS12615 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000020385.1:WP_012470593.1
          Length = 491

 Score =  477 bits (1228), Expect = e-139
 Identities = 249/491 (50%), Positives = 335/491 (68%), Gaps = 14/491 (2%)

Query: 4   EEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSMIGL 63
           ++F +LA  G N +P+  E +AD DTP++ + K+ D   S+LLES++GGEKW RY+ +G 
Sbjct: 7   KDFCQLAQKG-NLVPVYREIMADMDTPVTAFRKIDDDCYSFLLESIEGGEKWARYTFLGS 65

Query: 64  PSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLVGYF 123
               V+R  G  V  +  GV + S  V DPL  + +   R+   ++PGLPRF GG VGY 
Sbjct: 66  SPSLVVRTKGKTVETIEHGV-ITSQTVADPLDSIRALLSRFTPVEVPGLPRFFGGAVGYL 124

Query: 124 GYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVD----PAEEQ 179
           GYD VR+ E     +  P  +   D   +V+D +++FDN++ K+  +         + E 
Sbjct: 125 GYDMVRHFEHL--PTQKPALIDAYDAYFLVTDTLIIFDNVSQKIKVVSNAHLGGTVSAED 182

Query: 180 AFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEP-EFRSSYTREDYENAVGRIKEYIL 238
           A+ +  AR++G++  LR P+ P        P+A +P E RS+ +RE+YE AV + KEY+ 
Sbjct: 183 AYAEALARIEGIIHKLRGPLPPA-----GAPEAVKPAELRSNISREEYEAAVEKAKEYVR 237

Query: 239 AGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVED 298
           AGD +QVVPSQR S    A P D+YR LR  NP+PYM+F       + G+SPEV+VR E 
Sbjct: 238 AGDIIQVVPSQRFSGTLSADPFDIYRVLRTLNPSPYMFFLRLDGTVIAGASPEVMVRKEG 297

Query: 299 NLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRL 358
               +RPIAGTRPRGAT E D  L ++LL+D KE AEH+ML+DLGRND+GRV +TG+V +
Sbjct: 298 TRAELRPIAGTRPRGATPEEDATLAEELLADPKERAEHVMLVDLGRNDLGRVCATGTVTV 357

Query: 359 TEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPV 418
           +E MVIERYS+VMHIVSNV G+L EG  A D +RA  PAGTLSGAPK+RAMEIIDELEPV
Sbjct: 358 SELMVIERYSHVMHIVSNVYGELAEGRDAFDLVRATFPAGTLSGAPKVRAMEIIDELEPV 417

Query: 419 KRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRR 478
           +R +YGGAVGYF+++GNMD AIAIRT VI DG +H+QAGGG+VADS PA EW+ET+NK  
Sbjct: 418 RREIYGGAVGYFSFSGNMDLAIAIRTLVIKDGMVHLQAGGGVVADSDPAAEWQETVNKAM 477

Query: 479 AMFRAVALAEQ 489
           A+ RA+ +AE+
Sbjct: 478 AVRRAIEIAER 488


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: 702
Number of extensions: 28
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: 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 WP_012470593.1 GLOV_RS12615 (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.15817.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-178  580.4   0.0   1.7e-178  580.2   0.0    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012470593.1  GLOV_RS12615 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012470593.1  GLOV_RS12615 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.2   0.0  1.7e-178  1.7e-178       2     455 .]      28     484 ..      27     484 .. 0.97

  Alignments for each domain:
  == domain 1  score: 580.2 bits;  conditional E-value: 1.7e-178
                                 TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelk 70 
                                               d  tp+++++k++ + +sfllEs+e +e+++Ry ++g +p l++++k+++++++e+   ++++++d+l+
  lcl|NCBI__GCF_000020385.1:WP_012470593.1  28 DMDTPVTAFRKIDDDCYSFLLESIEGGEKWARYTFLGSSPSLVVRTKGKTVETIEHGVITSQTVADPLD 96 
                                               788****************************************************9999********** PP

                                 TIGR00564  71 elrklleka.eesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvek 138
                                               ++r+ll+++   + ++l+  + ggavGylgyd+vr++e+l+++++  ++  d+++l+++t+i+fD+v++
  lcl|NCBI__GCF_000020385.1:WP_012470593.1  97 SIRALLSRFtPVEVPGLPR-FFGGAVGYLGYDMVRHFEHLPTQKPALIDAYDAYFLVTDTLIIFDNVSQ 164
                                               ********99899999998.99*********************************************** PP

                                 TIGR00564 139 kvilienarteaers...aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakak 204
                                               k+ +++na+    +s   a++ea ar+e ++++l+ +l +a   +  k+ ++ sn+++eeye++v+kak
  lcl|NCBI__GCF_000020385.1:WP_012470593.1 165 KIKVVSNAHLGGTVSaedAYAEALARIEGIIHKLRGPLPPAGAPEAVKPAELRSNISREEYEAAVEKAK 233
                                               ********9887777666889999999999999*99999987777888999****************** PP

                                 TIGR00564 205 eyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvet 273
                                               ey++aGdi+qvv+Sqr++  ++a+pf++Yr+LRt NPSpy+++l l+++ + g+SPE++v+ +g r e 
  lcl|NCBI__GCF_000020385.1:WP_012470593.1 234 EYVRAGDIIQVVPSQRFSGTLSADPFDIYRVLRTLNPSPYMFFLRLDGTVIAGASPEVMVRKEGTRAEL 302
                                               ********************************************************************* PP

                                 TIGR00564 274 rPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmH 342
                                               rPiAGtr+RGat+eeD++l+eeLlad+KerAEH+mLvDL+RND+g+v+ +g+v v+el+ ie+yshvmH
  lcl|NCBI__GCF_000020385.1:WP_012470593.1 303 RPIAGTRPRGATPEEDATLAEELLADPKERAEHVMLVDLGRNDLGRVCATGTVTVSELMVIERYSHVMH 371
                                               ********************************************************************* PP

                                 TIGR00564 343 ivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaia 411
                                               ivS+V Gel+++ +a+D +ra++PaGTlsGAPKvrAme+idelE+++R+iYgGavgy+sf g++d aia
  lcl|NCBI__GCF_000020385.1:WP_012470593.1 372 IVSNVYGELAEGRDAFDLVRATFPAGTLSGAPKVRAMEIIDELEPVRREIYGGAVGYFSFSGNMDLAIA 440
                                               ********************************************************************* PP

                                 TIGR00564 412 iRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallraie 455
                                               iRt+v+kdg++++qAg+G+VaDSdp aE++Et+nKa+a+ raie
  lcl|NCBI__GCF_000020385.1:WP_012470593.1 441 IRTLVIKDGMVHLQAGGGVVADSDPAAEWQETVNKAMAVRRAIE 484
                                               ****************************************9985 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: 10.33
//
[ok]

This GapMind analysis is from Apr 10 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:

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