Alignments for a candidate for trpE in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Caulobacter crescentus NA1000

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate CCNA_01972 CCNA_01972 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Caulo:CCNA_01972
          Length = 513

 Score =  383 bits (983), Expect = e-111
 Identities = 223/483 (46%), Positives = 294/483 (60%), Gaps = 31/483 (6%)

Query: 26  DFDTPLSIYLKLAD-QPNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHVSILHDGVE 84
           D +TP+S YLK+A  +P S+L ESV+GG   GRYS++ +    V R  G    I      
Sbjct: 29  DLETPVSAYLKIAQARPYSFLFESVEGGAWRGRYSIVTMNPDLVWRCRGDQAEIAEGDDI 88

Query: 85  VESHDVEDPLAFVESFKDRYKVA--DIP-GLPRFNGGLVGYFGYDCVRYVEKRLGVSPNP 141
                   P   ++S +D    +  D+P GLP    G+ G  GYD VR VE+   V  NP
Sbjct: 89  AAGRFTPQPGGALDSLRDLVARSRMDLPKGLPPMAAGVFGALGYDLVRLVERLPDV--NP 146

Query: 142 DPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDP----AEEQAFEQGQARLQGLLETLRQ 197
           D L +PD ++     V VFD +A ++     V P    + + A +  +AR++ ++  L +
Sbjct: 147 DALNLPDGIMTRPSIVAVFDAIAQEIILTTTVRPQAGVSAKAAHDAARARIEAVMADLHR 206

Query: 198 PITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQRMSIDFKA 257
           P+      D   P     +F +  +R DY   V + K+YI AGD  QVV S R    F  
Sbjct: 207 PLAH----DAPRPPRGPMDFTTPVSRADYAEVVAKAKDYIAAGDIFQVVASHRFRAPFDL 262

Query: 258 APIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGTRPRGATEE 317
            P  LYR+LR  NP+P+++F N   F++VGSSPE+LVR+ D  +T+RPIAGTRPRGAT E
Sbjct: 263 PPFALYRSLRRTNPSPFLFFLNLDGFNLVGSSPEILVRLRDGKITIRPIAGTRPRGATPE 322

Query: 318 ADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTG----------------SVRLTEK 361
            D ALE +LL+D KE AEHLML+DLGRNDVGRV+                   +VR+TE 
Sbjct: 323 EDAALEAELLADPKERAEHLMLLDLGRNDVGRVAMLNHHGRNAPPEQARPKGPNVRVTES 382

Query: 362 MVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRG 421
             IERYS+VMHIVSNV G   EG+  +D L A LPAGTLSGAPK+RAMEIIDELE  KRG
Sbjct: 383 FTIERYSHVMHIVSNVEGTAPEGVDPVDVLMAALPAGTLSGAPKVRAMEIIDELEVEKRG 442

Query: 422 V-YGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           + Y GAVGYF  +G +DT I +RTA++ DG ++VQAGGGIVADS P  E++ET++K RA+
Sbjct: 443 ISYAGAVGYFGADGAVDTCIVLRTALVKDGMMYVQAGGGIVADSDPDAEYDETLHKSRAL 502

Query: 481 FRA 483
            RA
Sbjct: 503 KRA 505


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: 716
Number of extensions: 40
Number of successful extensions: 7
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: 513
Length adjustment: 34
Effective length of query: 459
Effective length of database: 479
Effective search space:   219861
Effective search space used:   219861
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 CCNA_01972 CCNA_01972 (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.7527.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-189  616.0   0.0   2.7e-189  615.8   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01972  CCNA_01972 anthranilate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01972  CCNA_01972 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  615.8   0.0  2.7e-189  2.7e-189       2     454 ..      29     506 ..      28     507 .. 0.98

  Alignments for each domain:
  == domain 1  score: 615.8 bits;  conditional E-value: 2.7e-189
                             TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak....ieedel 69 
                                           d +tp+s+ylk+a+ r++sfl+Esve ++++gRyS++++np+l++++++++a+++e dd +a+    + + +l
  lcl|FitnessBrowser__Caulo:CCNA_01972  29 DLETPVSAYLKIAQaRPYSFLFESVEGGAWRGRYSIVTMNPDLVWRCRGDQAEIAEGDDIAAGrftpQPGGAL 101
                                           789***********99********************************************9999999999*** PP

                             TIGR00564  70 kelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvil 142
                                           ++lr+l+++ +++ ++  +p+++g++G+lgyd+vrlve+l++ ++d+l+lpd +++  + v+vfD++++++il
  lcl|FitnessBrowser__Caulo:CCNA_01972 102 DSLRDLVARSRMDLPKGLPPMAAGVFGALGYDLVRLVERLPDVNPDALNLPDGIMTRPSIVAVFDAIAQEIIL 174
                                           *********65555544499***************************************************** PP

                             TIGR00564 143 ienarteaers...aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakakeyikaGdi 212
                                           ++++r +a++s   a+++a+ar+e+++a+l+++l+++++++++ +++ft+ v++++y+e vakak+yi+aGdi
  lcl|FitnessBrowser__Caulo:CCNA_01972 175 TTTVRPQAGVSakaAHDAARARIEAVMADLHRPLAHDAPRPPRGPMDFTTPVSRADYAEVVAKAKDYIAAGDI 247
                                           **********999899999****************************************************** PP

                             TIGR00564 213 fqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGat 285
                                           fqvv+S+r++a+++++pf+lYr+LR++NPSp+l++l+l++f+lvgsSPE+lv++++ ++++rPiAGtr+RGat
  lcl|FitnessBrowser__Caulo:CCNA_01972 248 FQVVASHRFRAPFDLPPFALYRSLRRTNPSPFLFFLNLDGFNLVGSSPEILVRLRDGKITIRPIAGTRPRGAT 320
                                           ************************************************************************* PP

                             TIGR00564 286 keeDealeeeLladeKerAEHlmLvDLaRNDigkvaklg................svevkellkiekyshvmH 342
                                           +eeD+ale+eLlad+KerAEHlmL+DL+RND+g+va+l+                +v+v+e+++ie+yshvmH
  lcl|FitnessBrowser__Caulo:CCNA_01972 321 PEEDAALEAELLADPKERAEHLMLLDLGRNDVGRVAMLNhhgrnappeqarpkgpNVRVTESFTIERYSHVMH 393
                                           ************************************************************************* PP

                             TIGR00564 343 ivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgi.YgGavgylsfdgdvdtaiaiRt 414
                                           ivS+VeG++ +++++vD+l+aalPaGTlsGAPKvrAme+idelE+ekRgi Y+Gavgy+++dg+vdt+i++Rt
  lcl|FitnessBrowser__Caulo:CCNA_01972 394 IVSNVEGTAPEGVDPVDVLMAALPAGTLSGAPKVRAMEIIDELEVEKRGIsYAGAVGYFGADGAVDTCIVLRT 466
                                           ************************************************************************* PP

                             TIGR00564 415 mvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                           +++kdg++yvqAg+GiVaDSdp+aEy+Etl+K++al+ra+
  lcl|FitnessBrowser__Caulo:CCNA_01972 467 ALVKDGMMYVQAGGGIVADSDPDAEYDETLHKSRALKRAA 506
                                           *************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (513 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: 10.91
//
[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:

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