Aligments for a candidate for trpE in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for trpE in Escherichia coli BW25113

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate 15384 b1264 anthranilate synthase component I (NCBI)

Query= SwissProt::P00895
         (520 letters)



>lcl|FitnessBrowser__Keio:15384 b1264 anthranilate synthase
           component I (NCBI)
          Length = 520

 Score = 1029 bits (2660), Expect = 0.0
 Identities = 520/520 (100%), Positives = 520/520 (100%)

Query: 1   MQTQKPTLELLTCEGAYRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALR 60
           MQTQKPTLELLTCEGAYRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALR
Sbjct: 1   MQTQKPTLELLTCEGAYRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALR 60

Query: 61  ITALGDTVTIQALSGNGEALLALLDNALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCS 120
           ITALGDTVTIQALSGNGEALLALLDNALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCS
Sbjct: 61  ITALGDTVTIQALSGNGEALLALLDNALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCS 120

Query: 121 LSVFDAFRLLQNLLNVPKEEREAMFFGGLFSYDLVAGFEDLPQLSAENNCPDFCFYLAET 180
           LSVFDAFRLLQNLLNVPKEEREAMFFGGLFSYDLVAGFEDLPQLSAENNCPDFCFYLAET
Sbjct: 121 LSVFDAFRLLQNLLNVPKEEREAMFFGGLFSYDLVAGFEDLPQLSAENNCPDFCFYLAET 180

Query: 181 LMVIDHQKKSTRIQASLFAPNEEEKQRLTARLNELRQQLTEAAPPLPVVSVPHMRCECNQ 240
           LMVIDHQKKSTRIQASLFAPNEEEKQRLTARLNELRQQLTEAAPPLPVVSVPHMRCECNQ
Sbjct: 181 LMVIDHQKKSTRIQASLFAPNEEEKQRLTARLNELRQQLTEAAPPLPVVSVPHMRCECNQ 240

Query: 241 SDEEFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDND 300
           SDEEFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDND
Sbjct: 241 SDEEFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDND 300

Query: 301 FTLFGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELS 360
           FTLFGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELS
Sbjct: 301 FTLFGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELS 360

Query: 361 EHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRAC 420
           EHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRAC
Sbjct: 361 EHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRAC 420

Query: 421 MNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATV 480
           MNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATV
Sbjct: 421 MNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATV 480

Query: 481 QAGAGVVLDSVPQSEADETRNKARAVLRAIATAHHAQETF 520
           QAGAGVVLDSVPQSEADETRNKARAVLRAIATAHHAQETF
Sbjct: 481 QAGAGVVLDSVPQSEADETRNKARAVLRAIATAHHAQETF 520


Lambda     K      H
   0.320    0.135    0.391 

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: 910
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: 520
Length of database: 520
Length adjustment: 35
Effective length of query: 485
Effective length of database: 485
Effective search space:   235225
Effective search space used:   235225
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 15384 b1264 (anthranilate synthase component I (NCBI))
to HMM TIGR00565 (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/TIGR00565.hmm
# target sequence database:        /tmp/gapView.22197.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00565  [M=498]
Accession:   TIGR00565
Description: trpE_proteo: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.3e-285  933.0   0.0   2.7e-285  932.8   0.0    1.0  1  lcl|FitnessBrowser__Keio:15384  b1264 anthranilate synthase comp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15384  b1264 anthranilate synthase component I (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  932.8   0.0  2.7e-285  2.7e-285       1     498 []      17     515 ..      17     515 .. 1.00

  Alignments for each domain:
  == domain 1  score: 932.8 bits;  conditional E-value: 2.7e-285
                       TIGR00565   1 yiadptalfeklcqdrpatlllesaeieskddlkslllvdaalkitclgdivtikalsnnGeallkkldaalkalveav 79 
                                     y+++ptalf++lc+drpatlllesa+i+skddlkslllvd+al+it+lgd+vti+als+nGeall+ ld+al+a+ve++
  lcl|FitnessBrowser__Keio:15384  17 YRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALRITALGDTVTIQALSGNGEALLALLDNALPAGVESE 95 
                                     99***************************************************************************** PP

                       TIGR00565  80 qsenalvlrflkvkklldedakllsasvfdalrllkslkqkpkep.ealllgGlfsydlvanfedlpqlkakndnvpdf 157
                                     qs+n++vlrf++v++lldeda+l+s+svfda+rll++l+++pke+ ea+++gGlfsydlva+fedlpql+a+n n+pdf
  lcl|FitnessBrowser__Keio:15384  96 QSPNCRVLRFPPVSPLLDEDARLCSLSVFDAFRLLQNLLNVPKEErEAMFFGGLFSYDLVAGFEDLPQLSAEN-NCPDF 173
                                     ********************************************99**************************9.***** PP

                       TIGR00565 158 ifylaenlividhkeksveikaalfaer.eekqvaiakldlkeaqkskkadfvpkvsaasreveanlsdeefegvvkal 235
                                     +fylae+l+vidh++ks++i+a+lfa++ eekq+++a+l+++++q++++a+++p+vs++++++e+n+sdeef+gvv++l
  lcl|FitnessBrowser__Keio:15384 174 CFYLAETLMVIDHQKKSTRIQASLFAPNeEEKQRLTARLNELRQQLTEAAPPLPVVSVPHMRCECNQSDEEFGGVVRLL 252
                                     ***************************98899*********************************************** PP

                       TIGR00565 236 kkeikkGeifqvvpsrrfslecpetlaayyqlkksnPsPymfylkdedfilfGasPesalkydaesrqleiyPiaGtrp 314
                                     +k+i++Geifqvvpsrrfsl+cp++laayy+lkksnPsPymf+++d+df+lfGasPes+lkyda+srq+eiyPiaGtrp
  lcl|FitnessBrowser__Keio:15384 253 QKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDNDFTLFGASPESSLKYDATSRQIEIYPIAGTRP 331
                                     ******************************************************************************* PP

                       TIGR00565 315 rGkdadGnidrdldsrlelelrldhkeraehlmlvdlarndlarvcksgkryvaellkvdrysnvmhlvsrvvGelrke 393
                                     rG++adG++drdldsr+ele+r+dhke++ehlmlvdlarndlar+c++g+ryva+l+kvdrys+vmhlvsrvvGelr++
  lcl|FitnessBrowser__Keio:15384 332 RGRRADGSLDRDLDSRIELEMRTDHKELSEHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHD 410
                                     ******************************************************************************* PP

                       TIGR00565 394 ldalhayracmnmGtlsGaPkikalqliyqlenqrrgsyGGavGyltseGdldtcivirsalvkngiavvqaGaGvvld 472
                                     ldalhayracmnmGtlsGaPk++a+qli+++e++rrgsyGGavGy+t++Gdldtcivirsalv+ngia+vqaGaGvvld
  lcl|FitnessBrowser__Keio:15384 411 LDALHAYRACMNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATVQAGAGVVLD 489
                                     ******************************************************************************* PP

                       TIGR00565 473 svPqseadetrakaravlkairkvsl 498
                                     svPqseadetr+karavl+ai+++++
  lcl|FitnessBrowser__Keio:15384 490 SVPQSEADETRNKARAVLRAIATAHH 515
                                     ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (498 nodes)
Target sequences:                          1  (520 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.86
//
[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