Alignments for a candidate for trpE in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methylosarcina fibrata AML-C10

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_020565438.1 A3OW_RS0121060 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000372865.1:WP_020565438.1
          Length = 495

 Score =  614 bits (1584), Expect = e-180
 Identities = 300/492 (60%), Positives = 384/492 (78%), Gaps = 1/492 (0%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M  E+F + A +G+NRIP+  E LAD DTPLS YLKLAD   SYL ESV GGE+WGRYSI
Sbjct: 1   MTPEQFNQYAREGFNRIPIIREVLADLDTPLSAYLKLADGAYSYLFESVHGGEQWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLPC+TV+R+   Q+ +  +G + +     +PL ++E+FK  Y+VP +  LPRF+GGLV
Sbjct: 61  IGLPCQTVIRITGKQISLEKNGRKEQTITHENPLLWIEQFKEGYKVPDIAHLPRFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYFGY+ + Y+E RL     PDPLGNPDI+LMVS+ ++VFDNL+GK+  +  A+P EE A
Sbjct: 121 GYFGYETIGYIEPRLGNSRKPDPLGNPDIVLMVSEEMLVFDNLSGKLLLLTHANPEEERA 180

Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAG 240
           +ER +ARL EL  +LR+ +  R        +  E  F + FT++ +E+AV + KDYI  G
Sbjct: 181 FERAEARLSELARKLRE-VQARPARHPSPKKVNESDFVSGFTQQGFEDAVRKAKDYITDG 239

Query: 241 DCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGL 300
           D MQVV SQR+SI + A P++LYRALRC NP+PYM++ N GDFH+VGSSPE+LVR+ED +
Sbjct: 240 DIMQVVLSQRLSIPYTAEPLNLYRALRCLNPSPYMFYLNLGDFHIVGSSPEILVRLEDNI 299

Query: 301 VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTE 360
           VTVRPIAGTR RG  +E DLALE++LL+D KEIAEHLMLIDLGRND GRV++IG+V++T+
Sbjct: 300 VTVRPIAGTRRRGATQEQDLALEKELLADPKEIAEHLMLIDLGRNDAGRVAEIGSVQLTD 359

Query: 361 KMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           KM++ERYS+VMHIVSNV G+L+ G +A D L A  PAGT+SGAPKIRAMEIIDELEPVKR
Sbjct: 360 KMIVERYSHVMHIVSNVIGRLKPGKNAFDVLAATFPAGTVSGAPKIRAMEIIDELEPVKR 419

Query: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           GVY GA+GY+AW+GN+DTAIAIRTAVIKN  LH+QAG GIV DS+P  EW+ET+NK RA+
Sbjct: 420 GVYSGAIGYIAWSGNLDTAIAIRTAVIKNNMLHIQAGAGIVYDSIPRNEWDETMNKGRAI 479

Query: 481 FRAVALAEQSVE 492
           FRAV++AE  +E
Sbjct: 480 FRAVSMAEAGLE 491


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: 727
Number of extensions: 21
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: 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_020565438.1 A3OW_RS0121060 (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.3588988.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-176  572.3   0.0   4.9e-176  572.1   0.0    1.0  1  NCBI__GCF_000372865.1:WP_020565438.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000372865.1:WP_020565438.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.1   0.0  4.9e-176  4.9e-176       2     454 ..      26     483 ..      25     484 .. 0.93

  Alignments for each domain:
  == domain 1  score: 572.1 bits;  conditional E-value: 4.9e-176
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ieedelkel 72 
                                           d  tp+s+ylkla  ++s+l+Esv+ +e++gRyS+igl  +++i+ +++ ++ le+++++++  ++e++l  +
  NCBI__GCF_000372865.1:WP_020565438.1  26 DLDTPLSAYLKLADGAYSYLFESVHGGEQWGRYSIIGLPCQTVIRITGK-QISLEKNGRKEQtiTHENPLLWI 97 
                                           778**********99***********************99999999986.66677777666645667777777 PP

                             TIGR00564  73 rkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhvekkvi 141
                                           +++ e ++   +++   + + gg+vGy+gy+t+ ++e+     +++d+l  pd++l++ e+++vfD+ + k++
  NCBI__GCF_000372865.1:WP_020565438.1  98 EQFKEGYK--VPDIAhlPRFNGGLVGYFGYETIGYIEPRLGnsRKPDPLGNPDIVLMVSEEMLVFDNLSGKLL 168
                                           77766653..333334467******************87553355**************************** PP

                             TIGR00564 142 lienarteaersaeeeaaarleellaelqkelekavkaleekkes...ftsnvekeeyeekvakakeyikaGd 211
                                           l+++a+ e+er a+e a+arl+el+++l++ +++ ++ + +kk++   f s ++++ +e++v+kak+yi++Gd
  NCBI__GCF_000372865.1:WP_020565438.1 169 LLTHANPEEER-AFERAEARLSELARKLREVQARPARHPSPKKVNesdFVSGFTQQGFEDAVRKAKDYITDGD 240
                                           *****999999.9***************99998887777766665667************************* PP

                             TIGR00564 212 ifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGa 284
                                           i+qvvlSqrl+ + +a+p++lYr+LR  NPSpy++yl+l df++vgsSPE+lv+++++ v++rPiAGtr+RGa
  NCBI__GCF_000372865.1:WP_020565438.1 241 IMQVVLSQRLSIPYTAEPLNLYRALRCLNPSPYMFYLNLGDFHIVGSSPEILVRLEDNIVTVRPIAGTRRRGA 313
                                           ************************************************************************* PP

                             TIGR00564 285 tkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdelta 357
                                           t+e+D ale+eLlad+Ke AEHlmL+DL+RND g+va++gsv+ ++ + +e+yshvmHivS+V G+lk++++a
  NCBI__GCF_000372865.1:WP_020565438.1 314 TQEQDLALEKELLADPKEIAEHLMLIDLGRNDAGRVAEIGSVQLTDKMIVERYSHVMHIVSNVIGRLKPGKNA 386
                                           ************************************************************************* PP

                             TIGR00564 358 vDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGi 430
                                           +D+l a++PaGT+sGAPK+rAme+idelE++kRg+Y+Ga+gy+   g++dtaiaiRt+v+k++++++qAgaGi
  NCBI__GCF_000372865.1:WP_020565438.1 387 FDVLAATFPAGTVSGAPKIRAMEIIDELEPVKRGVYSGAIGYIAWSGNLDTAIAIRTAVIKNNMLHIQAGAGI 459
                                           ************************************************************************* PP

                             TIGR00564 431 VaDSdpeaEyeEtlnKakallrai 454
                                           V+DS p +E++Et+nK +a  ra+
  NCBI__GCF_000372865.1:WP_020565438.1 460 VYDSIPRNEWDETMNKGRAIFRAV 483
                                           *******************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 31.70
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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