Alignments for a candidate for trpE in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Dinoroseobacter shibae DFL-12

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate 3608396 Dshi_1796 anthranilate synthase component I (RefSeq)

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__Dino:3608396
          Length = 509

 Score =  415 bits (1067), Expect = e-120
 Identities = 246/480 (51%), Positives = 307/480 (63%), Gaps = 26/480 (5%)

Query: 25  ADFDTPLSIYLKLADA-PNSYLLESVQGGEKWGRYSIIGLPCRTVLRVYDHQVRISIDGV 83
           AD DTP+S+ LKLA A  +S++LESV GGE  GRYS++GL    +        RI+    
Sbjct: 28  ADLDTPVSLMLKLAGARKDSFMLESVTGGEVRGRYSVVGLKPDLIWECRGTGARIN---- 83

Query: 84  ETERFDC-------ADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFGYDCVRYVEKRLA 136
            + RFD         DPLA +    A  ++     LP    GL GY GYD +R VE    
Sbjct: 84  RSARFDAEAFEDIPGDPLAALRALIAESRIEMPDELPAIAAGLFGYLGYDMIRLVEHLPN 143

Query: 137 TCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAI--VLAD------PSEENAYERGQARL 188
              NPDPLG PD +L+    V V D + G++  +  V A+       S   AY +   R+
Sbjct: 144 V--NPDPLGLPDAVLVRPSVVAVLDGVKGEVTVVSPVWANGSAGGGQSARAAYAQAAERV 201

Query: 189 EELLERL-RQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGDCMQVVP 247
            + +  L R  +  RR L  EAA+  EP   ++F   DY  AV R KDYI AGD  QVVP
Sbjct: 202 MDAVRDLERSAMAERRDLG-EAAELGEPV--SNFAHADYLAAVERAKDYIRAGDIFQVVP 258

Query: 248 SQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLVTVRPIA 307
           SQR S  F   P  LYR+LR  NP+P+M++FNFG F +VG+SPE+LVRV    VT+RPIA
Sbjct: 259 SQRWSQAFPLPPFALYRSLRRTNPSPFMFYFNFGGFQIVGASPEILVRVFGREVTIRPIA 318

Query: 308 GTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERY 367
           GTRPRG     D ALE DLL+DAKE AEHLML+DLGRNDVGRV+ IG V+ TE+ +IERY
Sbjct: 319 GTRPRGATPAEDDALEADLLADAKECAEHLMLLDLGRNDVGRVAKIGTVRPTEQFIIERY 378

Query: 368 SNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAV 427
           S+VMHIVSNV G+L E   A+ AL A LPAGT+SGAPK+RAMEIIDELEP KRGVYGG  
Sbjct: 379 SHVMHIVSNVVGELSEEHDALSALLAGLPAGTVSGAPKVRAMEIIDELEPEKRGVYGGGC 438

Query: 428 GYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALA 487
           GY A NG+MD  IA+RTAV+K+  L++QAGGG+V DS P  E++ET+NK +A+  A   A
Sbjct: 439 GYFAANGDMDMCIALRTAVVKDETLYIQAGGGVVYDSDPEAEFQETVNKAKAIRMAAQQA 498


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: 687
Number of extensions: 36
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: 492
Length of database: 509
Length adjustment: 34
Effective length of query: 458
Effective length of database: 475
Effective search space:   217550
Effective search space used:   217550
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 3608396 Dshi_1796 (anthranilate synthase component I (RefSeq))
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.16430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.8e-171  554.6   0.0   1.2e-170  554.4   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608396  Dshi_1796 anthranilate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608396  Dshi_1796 anthranilate synthase component I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.4   0.0  1.2e-170  1.2e-170       2     453 ..      29     494 ..      28     496 .. 0.91

  Alignments for each domain:
  == domain 1  score: 554.4 bits;  conditional E-value: 1.2e-170
                         TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak....ieedelkelr 73 
                                       d  tp+s++lkla  rk sf+lEsv+ +e +gRyS++gl+p+l +++++  a + + +  +a+    i +d+l +lr
  lcl|FitnessBrowser__Dino:3608396  29 DLDTPVSLMLKLAGaRKDSFMLESVTGGEVRGRYSVVGLKPDLIWECRGTGARINRSARFDAEafedIPGDPLAALR 105
                                       778***********99*******************************9984444333322222345799******** PP

                         TIGR00564  74 kllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvilienartea 150
                                       +l+++ +++ ++  +++++g++Gylgyd++rlve+l++ ++d+l lpd++l+  + v+v D v+ +v++++ +  + 
  lcl|FitnessBrowser__Dino:3608396 106 ALIAESRIEMPDELPAIAAGLFGYLGYDMIRLVEHLPNVNPDPLGLPDAVLVRPSVVAVLDGVKGEVTVVSPVWANG 182
                                       *****97776666677******************************************************9997776 PP

                         TIGR00564 151 ers.......aeeeaaarleellaelqkelekavkaleekkes..ftsnvekeeyeekvakakeyikaGdifqvvlS 218
                                       +         a+++aa+r+ + +++l++++  + + l e++e     sn+ +++y ++v++ak+yi+aGdifqvv+S
  lcl|FitnessBrowser__Dino:3608396 183 SAGggqsaraAYAQAAERVMDAVRDLERSAMAERRDLGEAAELgePVSNFAHADYLAAVERAKDYIRAGDIFQVVPS 259
                                       6656666665666667777777777777766553333333322467899999************************* PP

                         TIGR00564 219 qrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeee 295
                                       qr ++ + ++pf+lYr+LR++NPSp+++y+++ +f++vg+SPE+lv+v g++v++rPiAGtr+RGat++eD+ale++
  lcl|FitnessBrowser__Dino:3608396 260 QRWSQAFPLPPFALYRSLRRTNPSPFMFYFNFGGFQIVGASPEILVRVFGREVTIRPIAGTRPRGATPAEDDALEAD 336
                                       ***************************************************************************** PP

                         TIGR00564 296 LladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsG 372
                                       Llad Ke+AEHlmL+DL+RND+g+vak+g+v+ +e + ie+yshvmHivS+V+Gel +e +a+ al a lPaGT+sG
  lcl|FitnessBrowser__Dino:3608396 337 LLADAKECAEHLMLLDLGRNDVGRVAKIGTVRPTEQFIIERYSHVMHIVSNVVGELSEEHDALSALLAGLPAGTVSG 413
                                       ***************************************************************************** PP

                         TIGR00564 373 APKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKaka 449
                                       APKvrAme+idelE+ekRg+YgG+ gy+ ++gd+d++ia+Rt+v+kd+++y+qAg+G+V+DSdpeaE++Et+nKaka
  lcl|FitnessBrowser__Dino:3608396 414 APKVRAMEIIDELEPEKRGVYGGGCGYFAANGDMDMCIALRTAVVKDETLYIQAGGGVVYDSDPEAEFQETVNKAKA 490
                                       ***************************************************************************** PP

                         TIGR00564 450 llra 453
                                          a
  lcl|FitnessBrowser__Dino:3608396 491 IRMA 494
                                       8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (509 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: 7.56
//
[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