Alignments for a candidate for trpE in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Cupriavidus basilensis 4G11

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate RR42_RS18295 RR42_RS18295 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Cup4G11:RR42_RS18295
          Length = 505

 Score =  516 bits (1328), Expect = e-151
 Identities = 267/499 (53%), Positives = 348/499 (69%), Gaps = 22/499 (4%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQP----NSYLLESVQGGEKWG 56
           M   EF  LA  GYNRIPL  E  AD +TPLS+YLKLA       N++LLESV GGE++G
Sbjct: 1   MTELEFKSLAEQGYNRIPLITEAFADLETPLSLYLKLAQSQTRGVNTFLLESVVGGERFG 60

Query: 57  RYSMIGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFN 116
           RYS IGL +RT++R  G    ++ DG  VE+H+  +PL F+  F+ R+KVA  PGLPRF 
Sbjct: 61  RYSFIGLHARTLLRASGMRTEVVTDGRVVETHE-GNPLDFIADFEKRFKVALRPGLPRFC 119

Query: 117 GGLVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPA 176
           GGL GYFGYD VRY+EK+L  +  PD L +PDI L++ + + V DNL+GK++ IV  DP 
Sbjct: 120 GGLAGYFGYDTVRYIEKKLANTQKPDDLNLPDIQLLLCEELAVIDNLSGKLYLIVYADPT 179

Query: 177 EEQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEY 236
             +A+ + + RL+ L   LRQP+     + ++ P      +R  + + DY  AV + KEY
Sbjct: 180 TPEAYARARQRLRELRMKLRQPVD----VPITSPSVQTDVYRE-FEKADYLAAVHKAKEY 234

Query: 237 ILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRV 296
           I+AGD MQV   QR+   ++ +P+ LYRALR  NP+PYMYF+NFGDF +VG+SPE+LVR 
Sbjct: 235 IMAGDMMQVQIGQRLVKPYRDSPLTLYRALRSLNPSPYMYFYNFGDFQIVGASPEILVRQ 294

Query: 297 E------------DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGR 344
           E            D++VT+RP+AGTR RG T E D  L  +LL+D KEIAEH+MLIDL R
Sbjct: 295 ETRRVGSNGDQREDHIVTIRPLAGTRARGNTPEKDAQLATELLNDPKEIAEHVMLIDLAR 354

Query: 345 NDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAP 404
           ND+GR++  GSV++T++MVIE+YS+V HIVS+V G L+ G++ +D LRA  PAGTLSGAP
Sbjct: 355 NDIGRIAEIGSVKVTDQMVIEKYSHVQHIVSSVEGTLKPGMSNLDVLRATFPAGTLSGAP 414

Query: 405 KIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADS 464
           K+ AMEIIDELEP KRG+YGGAVGY ++ G MD AIAIRT ++ DG L+VQA  GIVADS
Sbjct: 415 KVHAMEIIDELEPRKRGIYGGAVGYLSFGGEMDLAIAIRTGIVKDGNLYVQAAAGIVADS 474

Query: 465 VPALEWEETINKRRAMFRA 483
            P  EW ET  K RA+ RA
Sbjct: 475 DPEAEWRETEAKARAVIRA 493


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: 684
Number of extensions: 30
Number of successful extensions: 5
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: 505
Length adjustment: 34
Effective length of query: 459
Effective length of database: 471
Effective search space:   216189
Effective search space used:   216189
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 RR42_RS18295 RR42_RS18295 (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.6309.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-168  545.1   0.0   9.1e-168  544.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS18295  RR42_RS18295 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS18295  RR42_RS18295 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.9   0.0  9.1e-168  9.1e-168       1     454 [.      25     494 ..      25     495 .. 0.93

  Alignments for each domain:
  == domain 1  score: 544.9 bits;  conditional E-value: 9.1e-168
                                 TIGR00564   1 adtltpisvylklak.r...kesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.i 64 
                                               ad +tp+s+ylkla+ +    ++fllEsv  +e+ gRyS+igl+ ++ ++a++ +++ ++ d++  + +
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295  25 ADLETPLSLYLKLAQsQtrgVNTFLLESVVGGERFGRYSFIGLHARTLLRASGMRTEVVT-DGRVVEtH 92 
                                               5889**********965777799**************************99987444444.55544448 PP

                                 TIGR00564  65 eedelkelrklleka.eesedeldeplsggavGylgydtvrlveklke..eaedelelpdlllllvetv 130
                                               e+++l+ + ++ +++    +++l+  ++gg+ Gy+gydtvr++ek+ +  +++d+l+lpd+ lll+e++
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295  93 EGNPLDFIADFEKRFkVALRPGLPR-FCGGLAGYFGYDTVRYIEKKLAntQKPDDLNLPDIQLLLCEEL 160
                                               9*************95556777876.******************99874345***************** PP

                                 TIGR00564 131 ivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeek 199
                                               +v D+ + k++li +a  ++ + a++ a++rl+el  +l++++   ++  +  ++++  ++ek++y ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295 161 AVIDNLSGKLYLIVYADPTTPE-AYARARQRLRELRMKLRQPVDVPIT-SPSVQTDVYREFEKADYLAA 227
                                               ****************888877.999*****************76555.344556688*********** PP

                                 TIGR00564 200 vakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk. 267
                                               v+kakeyi aGd++qv++ qrl ++ + +p+ lYr+LR+ NPSpy+y+ ++ df++vg+SPE+lv+ + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295 228 VHKAKEYIMAGDMMQVQIGQRLVKPYRDSPLTLYRALRSLNPSPYMYFYNFGDFQIVGASPEILVRQEt 296
                                               *****************************************************************9877 PP

                                 TIGR00564 268 ..........gkr.vetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgs 325
                                                         +++ v++rP+AGtr RG+t+e+D++l++eLl+d+Ke AEH+mL+DLaRNDig++a++gs
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295 297 rrvgsngdqrEDHiVTIRPLAGTRARGNTPEKDAQLATELLNDPKEIAEHVMLIDLARNDIGRIAEIGS 365
                                               778777766544579****************************************************** PP

                                 TIGR00564 326 vevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYg 394
                                               v+v++ + iekyshv+HivS+VeG+lk++++++D+lra++PaGTlsGAPKv+Ame+idelE++kRgiYg
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295 366 VKVTDQMVIEKYSHVQHIVSSVEGTLKPGMSNLDVLRATFPAGTLSGAPKVHAMEIIDELEPRKRGIYG 434
                                               ********************************************************************* PP

                                 TIGR00564 395 GavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               Gavgylsf g++d aiaiRt ++kdg +yvqA+aGiVaDSdpeaE++Et  Ka+a+ ra+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18295 435 GAVGYLSFGGEMDLAIAIRTGIVKDGNLYVQAAAGIVADSDPEAEWRETEAKARAVIRAA 494
                                               ********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (505 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.19
//
[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