Alignments for a candidate for trpE in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methylobacterium nodulans ORS 2060

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_015932020.1 MNOD_RS26380 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000022085.1:WP_015932020.1
          Length = 504

 Score =  380 bits (977), Expect = e-110
 Identities = 228/484 (47%), Positives = 296/484 (61%), Gaps = 15/484 (3%)

Query: 19  LACETLADFDTPLSIYLKL--ADQPNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHV 76
           L    +AD +TP++ +LKL    +  ++LLESV+GG   GRYSMIGL    V R  G   
Sbjct: 22  LRATLVADLETPVAAFLKLKAGREGAAFLLESVEGGAVRGRYSMIGLDPDLVWRCSG-GT 80

Query: 77  SILHDGVEVESHDVEDPLAFVESFKDRYKVADIPG---LPRFNGGLVGYFGYDCVRYVEK 133
           +   D  +++   V D    ++S +D    + IPG   LP    GL GY GYD VR +E+
Sbjct: 81  AERADAPDLDRF-VPDDRPPLDSLRDLIAESAIPGDAALPPMAAGLFGYLGYDMVREMER 139

Query: 134 RLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQ----AFEQGQARLQ 189
                P PDP+GVPD +L+    +VVFD +  ++  +  + P   Q    A E    RL+
Sbjct: 140 L--DPPKPDPIGVPDAILVRPTVMVVFDAVRDEIAVVTPLRPVPGQPAKAACEAALNRLE 197

Query: 190 GLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQ 249
            + ETL  P+      + +   A  P   S+ T E++   V R K YI AGD  QVV SQ
Sbjct: 198 RVAETLEGPLPVEAWANPTEIPAPAPV--SNTTPEEFHAMVARAKAYIAAGDIFQVVLSQ 255

Query: 250 RMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGT 309
           R    F      LYR+LR  NP P++ + +FG F +V SSPE+LVRV D  VT+RPIAGT
Sbjct: 256 RFEAPFALPAFALYRSLRRVNPAPFLCYLDFGTFQIVCSSPEILVRVRDGKVTIRPIAGT 315

Query: 310 RPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSN 369
           R RGAT E D AL ++LL+D KE AEHLML+DLGRNDVGRV+  GSV +T+   +E YS 
Sbjct: 316 RRRGATPEEDGALAEELLADPKERAEHLMLLDLGRNDVGRVAQIGSVTVTDSFFLEYYSQ 375

Query: 370 VMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGY 429
           VMHIVSNV G+L     A+ AL A  PAGT+SGAPK+RAM+IIDELE  KRG Y G +GY
Sbjct: 376 VMHIVSNVEGRLDPRHDALGALVAGFPAGTVSGAPKVRAMQIIDELEREKRGPYAGCIGY 435

Query: 430 FAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALAEQ 489
           F  +G MDT I +RTAV+ DG +HVQAG GIV DS PA E +E +NK +A FRA   A +
Sbjct: 436 FGADGQMDTCIVLRTAVVKDGRMHVQAGAGIVHDSDPASEQQECVNKAKAQFRAAEEAVR 495

Query: 490 TSAK 493
            +A+
Sbjct: 496 FAAQ 499


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: 711
Number of extensions: 42
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: 504
Length adjustment: 34
Effective length of query: 459
Effective length of database: 470
Effective search space:   215730
Effective search space used:   215730
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_015932020.1 MNOD_RS26380 (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.6861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-172  559.3   0.0   4.3e-172  559.1   0.0    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015932020.1  MNOD_RS26380 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015932020.1  MNOD_RS26380 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.1   0.0  4.3e-172  4.3e-172       1     454 [.      28     490 ..      28     491 .. 0.94

  Alignments for each domain:
  == domain 1  score: 559.1 bits;  conditional E-value: 4.3e-172
                                 TIGR00564   1 adtltpisvylklak..rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ie 65 
                                               ad +tp+ ++lkl+   + + fllEsve ++ +gRyS+igl+p+l++++++g+a++++a d +     +
  lcl|NCBI__GCF_000022085.1:WP_015932020.1  28 ADLETPVAAFLKLKAgrEGAAFLLESVEGGAVRGRYSMIGLDPDLVWRCSGGTAERADAPDLDRFvpDD 96 
                                               5889**********9844789*******************************99999987765554577 PP

                                 TIGR00564  66 edelkelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfD 134
                                                 +l++lr+l+++ ++  d   +p+++g++Gylgyd+vr +e+l ++++d++ +pd++l+  + ++vfD
  lcl|NCBI__GCF_000022085.1:WP_015932020.1  97 RPPLDSLRDLIAESAIPGDAALPPMAAGLFGYLGYDMVREMERLDPPKPDPIGVPDAILVRPTVMVVFD 165
                                               789**********98888888899********************************************* PP

                                 TIGR00564 135 hvekkvilienarteaers...aeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeye 197
                                               +v++++ +++  r   ++    a e+a +rle+++++l+ +l  +   +++ e  +    sn++ ee++
  lcl|NCBI__GCF_000022085.1:WP_015932020.1 166 AVRDEIAVVTPLRPVPGQPakaACEAALNRLERVAETLEGPLPVEawaNPT-EIPAPAPVSNTTPEEFH 233
                                               **********9998776655568899999*********9999876553333.34444466999****** PP

                                 TIGR00564 198 ekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkv 266
                                               + va+ak yi+aGdifqvvlSqr+ea++ +++f+lYr+LR+vNP+p+l yld+  f++v sSPE+lv+v
  lcl|NCBI__GCF_000022085.1:WP_015932020.1 234 AMVARAKAYIAAGDIFQVVLSQRFEAPFALPAFALYRSLRRVNPAPFLCYLDFGTFQIVCSSPEILVRV 302
                                               ********************************************************************* PP

                                 TIGR00564 267 kgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkie 335
                                               ++ +v++rPiAGtr+RGat+eeD al+eeLlad+KerAEHlmL+DL+RND+g+va++gsv v++++ +e
  lcl|NCBI__GCF_000022085.1:WP_015932020.1 303 RDGKVTIRPIAGTRRRGATPEEDGALAEELLADPKERAEHLMLLDLGRNDVGRVAQIGSVTVTDSFFLE 371
                                               ********************************************************************* PP

                                 TIGR00564 336 kyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdg 404
                                                ys vmHivS+VeG+l +  +a+ al a +PaGT+sGAPKvrAm++idelE ekRg+Y+G++gy+++dg
  lcl|NCBI__GCF_000022085.1:WP_015932020.1 372 YYSQVMHIVSNVEGRLDPRHDALGALVAGFPAGTVSGAPKVRAMQIIDELEREKRGPYAGCIGYFGADG 440
                                               ********************************************************************* PP

                                 TIGR00564 405 dvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               ++dt+i++Rt+v+kdg+++vqAgaGiV DSdp +E +E++nKaka+ ra+
  lcl|NCBI__GCF_000022085.1:WP_015932020.1 441 QMDTCIVLRTAVVKDGRMHVQAGAGIVHDSDPASEQQECVNKAKAQFRAA 490
                                               **********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (504 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: 00:00:00.03
# Mc/sec: 7.34
//
[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