Alignments for a candidate for trpE in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methylococcus capsulatus Bath

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_010961799.1 MCA_RS12660 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000008325.1:WP_010961799.1
          Length = 495

 Score =  626 bits (1614), Expect = 0.0
 Identities = 316/496 (63%), Positives = 381/496 (76%), Gaps = 10/496 (2%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M  E F   AA GYNR+PL+   LAD DTPLS YLKLAD P SYL ESV GGE+WGRYSI
Sbjct: 1   MTPERFQAFAAQGYNRVPLARRVLADLDTPLSAYLKLADGPYSYLFESVHGGEQWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLPCRT + V  H+V +  DG   E     +PLA+++ F +R++VP + GLPRF GGLV
Sbjct: 61  IGLPCRTCIEVRGHEVIVLRDGARAETLTVENPLAWIKAFGSRFKVPDLEGLPRFTGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYFGY+ + Y+E RLA    PDP+G+PDILLMVS+ V+VFD L GK+  +V ADP+E  A
Sbjct: 121 GYFGYETMGYIEPRLAKT-KPDPIGSPDILLMVSEEVLVFDKLTGKLLVVVHADPNEAGA 179

Query: 181 YERGQARLEELLERLRQ----PITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDY 236
           Y + Q RL+EL+  LR     P  PR    ++ A      F + FTRE +E+AV R+K+Y
Sbjct: 180 YAKAQTRLDELVRELRSRQLPPAPPRSPRTVDEAD-----FISGFTREGFEDAVRRVKEY 234

Query: 237 ILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRV 296
           I+ GD MQVV SQR+SI + A+P+DLYRALRC NP+PYMY  N GDFHVVGSSPE+LVR+
Sbjct: 235 IVEGDVMQVVLSQRLSIPYAASPLDLYRALRCLNPSPYMYQLNLGDFHVVGSSPEILVRL 294

Query: 297 EDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAV 356
           EDG VTVRPIAGTR RG + E D ALE++LL+D KE+AEHLMLIDLGRND GR+S+ G+V
Sbjct: 295 EDGTVTVRPIAGTRRRGRSPEEDQALERELLADPKELAEHLMLIDLGRNDTGRISETGSV 354

Query: 357 KVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELE 416
           ++TEKMV+ERYS+VMHIVSNVTG+L+ G  A D L A  PAGT+SGAPKIRAMEII ELE
Sbjct: 355 RLTEKMVVERYSHVMHIVSNVTGKLQAGKDAYDVLAATFPAGTVSGAPKIRAMEIIAELE 414

Query: 417 PVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINK 476
           PVKRGVY GAVGY+ W+GNMDTAIAIRTAVIK+G LH+QAG G+V DSVP  EWEET+NK
Sbjct: 415 PVKRGVYSGAVGYIGWSGNMDTAIAIRTAVIKDGRLHIQAGAGVVYDSVPRSEWEETMNK 474

Query: 477 RRAMFRAVALAEQSVE 492
            RA+FRAVA+AE  VE
Sbjct: 475 ARAIFRAVAMAEAGVE 490


Lambda     K      H
   0.321    0.139    0.408 

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: 750
Number of extensions: 31
Number of successful extensions: 3
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: 492
Length of database: 495
Length adjustment: 34
Effective length of query: 458
Effective length of database: 461
Effective search space:   211138
Effective search space used:   211138
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_010961799.1 MCA_RS12660 (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.23458.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-174  566.4   0.0   3.1e-174  566.2   0.0    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010961799.1  MCA_RS12660 anthranilate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010961799.1  MCA_RS12660 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.2   0.0  3.1e-174  3.1e-174       2     454 ..      26     482 ..      25     483 .. 0.93

  Alignments for each domain:
  == domain 1  score: 566.2 bits;  conditional E-value: 3.1e-174
                                 TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedel 69 
                                               d  tp+s+ylkla  ++s+l+Esv+ +e++gRyS+igl  ++ i++++++++ l+   ++++ ++e++l
  lcl|NCBI__GCF_000008325.1:WP_010961799.1  26 DLDTPLSAYLKLADGPYSYLFESVHGGEQWGRYSIIGLPCRTCIEVRGHEVIVLRDGARAETlTVENPL 94 
                                               778**********99********************************9977777654444447899999 PP

                                 TIGR00564  70 kelrkllekaeesedeld..eplsggavGylgydtvrlveklkeea.edelelpdlllllvetvivfDh 135
                                                 ++++ ++++   ++l+  + ++gg+vGy+gy+t+ ++e+  +++ +d++  pd+ll++ e+v+vfD+
  lcl|NCBI__GCF_000008325.1:WP_010961799.1  95 AWIKAFGSRFK--VPDLEglPRFTGGLVGYFGYETMGYIEPRLAKTkPDPIGSPDILLMVSEEVLVFDK 161
                                               99999999965..666666678******************9877655********************** PP

                                 TIGR00564 136 vekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkes...ftsnvekeeyeekva 201
                                                + k++++ +a  ++   a+++a++rl+el++el++ + + ++   +++++   f s +++e +e++v+
  lcl|NCBI__GCF_000008325.1:WP_010961799.1 162 LTGKLLVVVHADPNEAG-AYAKAQTRLDELVRELRSRQLPPAPPRSPRTVDeadFISGFTREGFEDAVR 229
                                               *****999999666555.99**************99988875544444333455*************** PP

                                 TIGR00564 202 kakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkr 270
                                               ++keyi +Gd++qvvlSqrl+ +  a+p++lYr+LR  NPSpy+y l+l df++vgsSPE+lv++++ +
  lcl|NCBI__GCF_000008325.1:WP_010961799.1 230 RVKEYIVEGDVMQVVLSQRLSIPYAASPLDLYRALRCLNPSPYMYQLNLGDFHVVGSSPEILVRLEDGT 298
                                               ********************************************************************* PP

                                 TIGR00564 271 vetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekysh 339
                                               v++rPiAGtr+RG+++eeD+ale+eLlad+Ke AEHlmL+DL+RND g+++++gsv+ +e + +e+ysh
  lcl|NCBI__GCF_000008325.1:WP_010961799.1 299 VTVRPIAGTRRRGRSPEEDQALERELLADPKELAEHLMLIDLGRNDTGRISETGSVRLTEKMVVERYSH 367
                                               ********************************************************************* PP

                                 TIGR00564 340 vmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdt 408
                                               vmHivS+V+G+l+ +++a+D+l a++PaGT+sGAPK+rAme+i+elE++kRg+Y+Gavgy++  g++dt
  lcl|NCBI__GCF_000008325.1:WP_010961799.1 368 VMHIVSNVTGKLQAGKDAYDVLAATFPAGTVSGAPKIRAMEIIAELEPVKRGVYSGAVGYIGWSGNMDT 436
                                               ********************************************************************* PP

                                 TIGR00564 409 aiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               aiaiRt+v+kdg++++qAgaG+V+DS+p +E+eEt+nKa+a  ra+
  lcl|NCBI__GCF_000008325.1:WP_010961799.1 437 AIAIRTAVIKDGRLHIQAGAGVVYDSVPRSEWEETMNKARAIFRAV 482
                                               *****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (495 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: 8.06
//
[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