Aligments for a candidate for trpE in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Aligments for a candidate for trpE in Pseudomonas fluorescens FW300-N2E2

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate Pf6N2E2_4822 Anthranilate synthase, aminase component (EC 4.1.3.27)

Query= SwissProt::P20579
         (493 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 Anthranilate
           synthase, aminase component (EC 4.1.3.27)
          Length = 493

 Score =  875 bits (2260), Expect = 0.0
 Identities = 436/491 (88%), Positives = 456/491 (92%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           MNREEFLRLAA GYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYS+
Sbjct: 1   MNREEFLRLAAAGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSI 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLP RTV+RVH + VS+ HDGVE+ES +VEDPLAFVE+FK RY V  IPGLPRFNGGLV
Sbjct: 61  IGLPCRTVLRVHDHRVSVTHDGVEIESLEVEDPLAFVETFKARYNVPTIPGLPRFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           GYFGYDCVRYVEKRLG  PNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVL DP++E A
Sbjct: 121 GYFGYDCVRYVEKRLGTCPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLADPSQEDA 180

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
           +EQGQ  LQ LLE LRQPI PR GLD S   A +P FRSS+T++DYE AV  IKEYILAG
Sbjct: 181 YEQGQQSLQALLEKLRQPIAPRPGLDFSKQSATDPVFRSSFTQDDYERAVDTIKEYILAG 240

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300
           DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL
Sbjct: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300

Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360
           +TVRPIAGTRPRGATEEADRALE+DLLSDDKEIAEHLMLIDLGRND GRVS  GSV+LTE
Sbjct: 301 ITVRPIAGTRPRGATEEADRALEEDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTE 360

Query: 361 KMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           KMVIERYSNVMHIVSNV GQL+ GLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR
Sbjct: 361 KMVIERYSNVMHIVSNVTGQLKAGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420

Query: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           GVYGGAVGYFAWNGNMDTAIAIRTAVI +GELHVQAGGGIVADSVPALEWEET+NKRRAM
Sbjct: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETLNKRRAM 480

Query: 481 FRAVALAEQTS 491
           FRAVALAEQTS
Sbjct: 481 FRAVALAEQTS 491


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: 905
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: 493
Length of database: 493
Length adjustment: 34
Effective length of query: 459
Effective length of database: 459
Effective search space:   210681
Effective search space used:   210681
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 Pf6N2E2_4822 (Anthranilate synthase, aminase component (EC 4.1.3.27))
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.31324.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     1e-176  574.3   0.0   1.2e-176  574.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822  Anthranilate synthase, aminase c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822  Anthranilate synthase, aminase component (EC 4.1.3.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.1   0.0  1.2e-176  1.2e-176       2     454 ..      26     484 ..      25     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: 574.1 bits;  conditional E-value: 1.2e-176
                                      TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.. 63 
                                                    d  tp+s+ylkla +++s+llEsv+ +e++gRyS+igl  +++++++d+++  +++d+ e++  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822  26 DFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVHDHRV-SVTHDGVEIEsl 88 
                                                    6679*******************************************9844.333343333334 PP

                                      TIGR00564  64 ieedelkelrkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdll 123
                                                    ++ed+l  ++++ +++  + + ++  + + gg+vGy+gyd+vr+vek     +++d+l +pd+l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822  89 EVEDPLAFVETFKARY--NVPTIPglPRFNGGLVGYFGYDCVRYVEKRLGtcPNPDPLGVPDIL 150
                                                    7888888777777765..4455555556******************98664466********** PP

                                      TIGR00564 124 lllvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkeleka..vkaleekke 185
                                                    l++ + v+vfD+ + k++ i  a  ++e +a+e+ ++ l++ll++l+++++++      + k+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 151 LMVSDAVVVFDNLAGKMHAIVLADPSQE-DAYEQGQQSLQALLEKLRQPIAPRpgL--DFSKQS 211
                                                    **********************966655.59********************99553..444443 PP

                                      TIGR00564 186 s....ftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpyl 245
                                                         f s++++++ye +v+++keyi aGd +qvv+Sqr++ +++a p++lYr+LR  NP py+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 212 AtdpvFRSSFTQDDYERAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYM 275
                                                    344779********************************************************** PP

                                      TIGR00564 246 yyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmL 309
                                                    y++++ df++vgsSPE+lv+v+++ +++rPiAGtr+RGat+e+D+alee+Ll+d Ke AEHlmL
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 276 YFFNFGDFHVVGSSPEVLVRVEDNLITVRPIAGTRPRGATEEADRALEEDLLSDDKEIAEHLML 339
                                                    **************************************************************** PP

                                      TIGR00564 310 vDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGA 373
                                                    +DL+RND g+v+++gsv+ +e + ie+ys vmHivS+V+G+lk +lta+Dalra+lPaGTlsGA
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 340 IDLGRNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQLKAGLTAMDALRAILPAGTLSGA 403
                                                    **************************************************************** PP

                                      TIGR00564 374 PKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpe 437
                                                    PK+rAme+idelE++kRg+YgGavgy+  +g++dtaiaiRt+v+k+g ++vqAg+GiVaDS+p 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 404 PKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPA 467
                                                    **************************************************************** PP

                                      TIGR00564 438 aEyeEtlnKakallrai 454
                                                     E+eEtlnK +a+ ra+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822 468 LEWEETLNKRRAMFRAV 484
                                                    *************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (493 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: 8.02
//
[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