Aligments for a candidate for trpE in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Aligments for a candidate for trpE in Sphingomonas koreensis DSMZ 15582

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate Ga0059261_0256 Ga0059261_0256 anthranilate synthase component I, non-proteobacterial lineages

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Korea:Ga0059261_0256
          Length = 508

 Score =  355 bits (910), Expect = e-102
 Identities = 218/474 (45%), Positives = 282/474 (59%), Gaps = 26/474 (5%)

Query: 24  LADFDTPLSIYLKLADQPNS-YLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHVSILHDG 82
           LAD DTP+S  LKL +     +LLESV+GG   GR+S+IGL    V R HG    I  + 
Sbjct: 32  LADTDTPVSAALKLIEPGRGDFLLESVEGGAVRGRHSLIGLAPDLVFRAHGQQAEI--NP 89

Query: 83  VEVESHDVEDPLA--FVESFKDRYKVA--DIPG-LPRFNGGLVGYFGYDCVRYVEKRLGV 137
             +   D   P A   +E+ +   +    D+P  LPR    LVGYFGY+ +  VE     
Sbjct: 90  FWLTDRDAFAPAAQPTLEALRTLVQSCRMDVPAELPRALACLVGYFGYETIGLVETL--P 147

Query: 138 SPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQAFEQGQARLQGLLETL-- 195
             + D LG+PD++ +    +++FD LA    ++ LV P    +    +ARL    E +  
Sbjct: 148 RADEDALGLPDMIFVRPTVILIFDRLAD---SLFLVAPVWPGSTRDPEARLADAAERIDA 204

Query: 196 ------RQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQ 249
                   P+ P+   D     A E   R +    DY   V R KEYI AGD  QVV +Q
Sbjct: 205 TAARLATAPLPPKVAGD-----ALEIAARPTLADGDYAAMVARAKEYITAGDIFQVVLAQ 259

Query: 250 RMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGT 309
           R +  F   PI+LYRALR  NP+P++YF +   F + GSSPE+LVRV D+ VT+RPIAGT
Sbjct: 260 RFTAPFALPPIELYRALRRVNPSPFLYFLDLPGFALTGSSPEILVRVRDDEVTIRPIAGT 319

Query: 310 RPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSN 369
           RPRG T   D A    LL+D KE AEHLML+DLGRND GRV+  G+VR+T+   +E YS+
Sbjct: 320 RPRGKTAAEDEANRTSLLADPKERAEHLMLLDLGRNDTGRVAQAGTVRVTDSYTVEFYSH 379

Query: 370 VMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGY 429
           VMHIVSNV G+LR    A+DAL A  PAGT+SGAPK+RA EII ELE  +RG Y G VGY
Sbjct: 380 VMHIVSNVVGKLRPDADALDALFAGFPAGTVSGAPKVRACEIIAELEREQRGPYAGGVGY 439

Query: 430 FAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRA 483
           F+ +G+MD+ I +RTA++ DG +HV AG GIVADS  A E  E   K  A+F A
Sbjct: 440 FSPDGSMDSCIVLRTAIVKDGTMHVTAGAGIVADSDAAYEQRECEAKAGALFAA 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: 676
Number of extensions: 33
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: 508
Length adjustment: 34
Effective length of query: 459
Effective length of database: 474
Effective search space:   217566
Effective search space used:   217566
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 Ga0059261_0256 Ga0059261_0256 (anthranilate synthase component I, non-proteobacterial lineages)
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.3848.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-160  518.7   0.0     9e-160  518.5   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0256  Ga0059261_0256 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0256  Ga0059261_0256 anthranilate synthase component I, non-proteobacterial linea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.5   0.0    9e-160    9e-160       1     453 [.      33     493 ..      33     495 .. 0.93

  Alignments for each domain:
  == domain 1  score: 518.5 bits;  conditional E-value: 9e-160
                                 TIGR00564   1 adtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkav....lleaddeeaki 64 
                                               adt tp+s++lkl +  +  fllEsve ++ +gR+Sligl p+l+++a++++a+    +l+ +d  a  
  lcl|FitnessBrowser__Korea:Ga0059261_0256  33 ADTDTPVSAALKLIEpGRGDFLLESVEGGAVRGRHSLIGLAPDLVFRAHGQQAEinpfWLTDRDAFAPA 101
                                               5899**********9889*****************************9998654111134444444448 PP

                                 TIGR00564  65 eedelkelrklleka.eesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetviv 132
                                                +  l++lr+l++++ +    el+ +  + +vGy+gy+t+ lve+l+++ ed+l lpd++++  + +++
  lcl|FitnessBrowser__Korea:Ga0059261_0256 102 AQPTLEALRTLVQSCrMDVPAELPRA-LACLVGYFGYETIGLVETLPRADEDALGLPDMIFVRPTVILI 169
                                               88999**********44445567765.578*************************************** PP

                                 TIGR00564 133 fDhvekkvilienarteaers...aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyee 198
                                               fD  +++++l++ +   + r+     ++aa+r+++++a+l ++  +   a    +    +++   +y++
  lcl|FitnessBrowser__Korea:Ga0059261_0256 170 FDRLADSLFLVAPVWPGSTRDpeaRLADAAERIDATAARLATAPLPPKVAGDALEIAARPTLADGDYAA 238
                                               *************9999888887778899999***99999998887766667777778899999***** PP

                                 TIGR00564 199 kvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk 267
                                                va+akeyi+aGdifqvvl+qr++a++ ++p+elYr+LR+vNPSp+ly+ldl +f l gsSPE+lv+v+
  lcl|FitnessBrowser__Korea:Ga0059261_0256 239 MVARAKEYITAGDIFQVVLAQRFTAPFALPPIELYRALRRVNPSPFLYFLDLPGFALTGSSPEILVRVR 307
                                               ********************************************************************* PP

                                 TIGR00564 268 gkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiek 336
                                               +++v++rPiAGtr+RG+t +eDea+++ Llad+KerAEHlmL+DL+RND g+va++g+v+v++++++e 
  lcl|FitnessBrowser__Korea:Ga0059261_0256 308 DDEVTIRPIAGTRPRGKTAAEDEANRTSLLADPKERAEHLMLLDLGRNDTGRVAQAGTVRVTDSYTVEF 376
                                               ********************************************************************* PP

                                 TIGR00564 337 yshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgd 405
                                               yshvmHivS+V+G+l+++++a+Dal a +PaGT+sGAPKvrA e+i+elE e+Rg+Y+G+vgy+s dg+
  lcl|FitnessBrowser__Korea:Ga0059261_0256 377 YSHVMHIVSNVVGKLRPDADALDALFAGFPAGTVSGAPKVRACEIIAELEREQRGPYAGGVGYFSPDGS 445
                                               ********************************************************************* PP

                                 TIGR00564 406 vdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallra 453
                                               +d++i++Rt+++kdg+++v AgaGiVaDSd   E +E+  Ka al  a
  lcl|FitnessBrowser__Korea:Ga0059261_0256 446 MDSCIVLRTAIVKDGTMHVTAGAGIVADSDAAYEQRECEAKAGALFAA 493
                                               *******************************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (508 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: 7.37
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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