Alignments for a candidate for trpE in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Pseudomonas stutzeri RCH2

Align anthranilate synthase (EC 4.1.3.27) (characterized)
to candidate GFF3583 Psest_3650 anthranilate synthase component I, non-proteobacterial lineages

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__psRCH2:GFF3583
          Length = 494

 Score =  830 bits (2145), Expect = 0.0
 Identities = 413/489 (84%), Positives = 446/489 (91%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M REEFLRLAA+G+NRIPLSFETLADFDTPLS+YLKLADAPNSYLLESVQGGEKWGRYSI
Sbjct: 1   MTREEFLRLAAEGHNRIPLSFETLADFDTPLSLYLKLADAPNSYLLESVQGGEKWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLPCRTVLRV DH++ ++ DG+ETE  +  DPLAFVE F+ RY+V  V GLPRF+GGLV
Sbjct: 61  IGLPCRTVLRVRDHRISVTTDGIETEACEVEDPLAFVESFQQRYRVAPVEGLPRFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYFGYD VRYVE++L  CPNPDPLG PDILLMVSDAVVVFDNLAGK+H IVL DPS+  A
Sbjct: 121 GYFGYDSVRYVERKLGNCPNPDPLGTPDILLMVSDAVVVFDNLAGKLHCIVLVDPSQPEA 180

Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAG 240
           YE GQARL+ L  +LRQ ITPR GLD E + G EP FR+SF+REDYE AV RIKDYILAG
Sbjct: 181 YEAGQARLQALRAKLRQSITPRLGLDFEKSNGAEPTFRSSFSREDYEQAVNRIKDYILAG 240

Query: 241 DCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGL 300
           DCMQVV SQRMSI FKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVE+GL
Sbjct: 241 DCMQVVISQRMSIPFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEEGL 300

Query: 301 VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTE 360
           VTVRPIAGTRPRG +EEADLALEQDLLSDAKE+AEHLMLIDLGRNDVGRV++ G V++TE
Sbjct: 301 VTVRPIAGTRPRGASEEADLALEQDLLSDAKELAEHLMLIDLGRNDVGRVAETGTVRLTE 360

Query: 361 KMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           KMVIERYSNVMHIVSNVTGQL+  L+AMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR
Sbjct: 361 KMVIERYSNVMHIVSNVTGQLKAPLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420

Query: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           GVYGGAVGYLAWNGNMDTAIAIRTAVIK+GELHVQAG GIVADS PALEWEET+NKRRAM
Sbjct: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKDGELHVQAGAGIVADSQPALEWEETLNKRRAM 480

Query: 481 FRAVALAEQ 489
           FRAVALAE+
Sbjct: 481 FRAVALAER 489


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: 809
Number of extensions: 22
Number of successful extensions: 1
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: 494
Length adjustment: 34
Effective length of query: 458
Effective length of database: 460
Effective search space:   210680
Effective search space used:   210680
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 GFF3583 Psest_3650 (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.26779.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.4e-175  568.7   0.0   6.2e-175  568.5   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3583  Psest_3650 anthranilate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3583  Psest_3650 anthranilate synthase component I, non-proteobacterial lineages
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.5   0.0  6.2e-175  6.2e-175       2     454 ..      26     484 ..      25     485 .. 0.93

  Alignments for each domain:
  == domain 1  score: 568.5 bits;  conditional E-value: 6.2e-175
                           TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ieedelkelrk 74 
                                         d  tp+s+ylkla  ++s+llEsv+ +e++gRyS+igl  +++++++d+++  +++d+ e++  ++ed+l  +++
  lcl|FitnessBrowser__psRCH2:GFF3583  26 DFDTPLSLYLKLADAPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVRDHRIS-VTTDGIETEacEVEDPLAFVES 99 
                                         6679**********9********************************98544.4444444444589999999999 PP

                           TIGR00564  75 lleka.eesedeldeplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhvekkviliena 146
                                         + +++     ++l+  + gg+vGy+gyd vr+ve++    +++d+l +pd+ll++ + v+vfD+ + k++ i  +
  lcl|FitnessBrowser__psRCH2:GFF3583 100 FQQRYrVAPVEGLPR-FNGGLVGYFGYDSVRYVERKLGncPNPDPLGTPDILLMVSDAVVVFDNLAGKLHCIVLV 173
                                         999984445666665.******************98764456********************************* PP

                           TIGR00564 147 rteaersaeeeaaarleellaelqkelekavkaleekkes....ftsnvekeeyeekvakakeyikaGdifqvvl 217
                                           ++ + a+e+ +arl++l a+l+++++++    +ek++     f s++++e+ye++v+++k+yi aGd +qvv+
  lcl|FitnessBrowser__psRCH2:GFF3583 174 DPSQPE-AYEAGQARLQALRAKLRQSITPRLGLDFEKSNGaeptFRSSFSREDYEQAVNRIKDYILAGDCMQVVI 247
                                         777666.9********************99555555444333449****************************** PP

                           TIGR00564 218 SqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDeal 292
                                         Sqr++ +++a p++lYr+LR  NP py+y++++ df++vgsSPE+lv+v++  v++rPiAGtr+RGa++e+D al
  lcl|FitnessBrowser__psRCH2:GFF3583 248 SQRMSIPFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEEGLVTVRPIAGTRPRGASEEADLAL 322
                                         *************************************************9999********************** PP

                           TIGR00564 293 eeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPa 367
                                         e++Ll+d Ke AEHlmL+DL+RND+g+va++g+v+ +e + ie+ys vmHivS+V+G+lk  lta+Dalra+lPa
  lcl|FitnessBrowser__psRCH2:GFF3583 323 EQDLLSDAKELAEHLMLIDLGRNDVGRVAETGTVRLTEKMVIERYSNVMHIVSNVTGQLKAPLTAMDALRAILPA 397
                                         *************************************************************************** PP

                           TIGR00564 368 GTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeE 442
                                         GTlsGAPK+rAme+idelE++kRg+YgGavgyl  +g++dtaiaiRt+v+kdg ++vqAgaGiVaDS+p  E+eE
  lcl|FitnessBrowser__psRCH2:GFF3583 398 GTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKDGELHVQAGAGIVADSQPALEWEE 472
                                         *************************************************************************** PP

                           TIGR00564 443 tlnKakallrai 454
                                         tlnK +a+ ra+
  lcl|FitnessBrowser__psRCH2:GFF3583 473 TLNKRRAMFRAV 484
                                         ********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (494 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: 7.58
//
[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