Alignments for a candidate for trpE in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Klebsiella michiganensis M5al

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate BWI76_RS11860 BWI76_RS11860 anthranilate synthase component I

Query= SwissProt::P00895
         (520 letters)



>FitnessBrowser__Koxy:BWI76_RS11860
          Length = 520

 Score =  883 bits (2282), Expect = 0.0
 Identities = 442/520 (85%), Positives = 476/520 (91%)

Query: 1   MQTQKPTLELLTCEGAYRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALR 60
           MQT KP LELLT +  YR+NPTALFHQ+CG RPATLLLESADIDSKDDLKSLLLVDSALR
Sbjct: 1   MQTSKPALELLTSDAIYRENPTALFHQICGARPATLLLESADIDSKDDLKSLLLVDSALR 60

Query: 61  ITALGDTVTIQALSGNGEALLALLDNALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCS 120
           ITALGDTVTI ALS NG ALL LLD+ALP+G+ +++ PN RVL FPPVS LLDEDARLCS
Sbjct: 61  ITALGDTVTIHALSANGTALLELLDSALPSGINNQRQPNSRVLTFPPVSALLDEDARLCS 120

Query: 121 LSVFDAFRLLQNLLNVPKEEREAMFFGGLFSYDLVAGFEDLPQLSAENNCPDFCFYLAET 180
           LSVFDAFRLLQ L+ VP++EREAMFFGGLF+YDLVAGFEDLP L ++  CPD+CFYLAET
Sbjct: 121 LSVFDAFRLLQELVTVPQDEREAMFFGGLFAYDLVAGFEDLPSLESDTACPDYCFYLAET 180

Query: 181 LMVIDHQKKSTRIQASLFAPNEEEKQRLTARLNELRQQLTEAAPPLPVVSVPHMRCECNQ 240
           L+VIDHQ K+TRIQASLF P E EKQRL  R+ +LRQQL E   PLPV +V  MRC+C+Q
Sbjct: 181 LLVIDHQTKNTRIQASLFTPLESEKQRLLQRIAQLRQQLNEPPLPLPVTTVAEMRCDCDQ 240

Query: 241 SDEEFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDND 300
           SDEE+G VVR +Q+AIRAGEIFQVVPSRRFSLPCPSPLAAY VLKKSNPSPYMFFMQDND
Sbjct: 241 SDEEYGAVVRKMQRAIRAGEIFQVVPSRRFSLPCPSPLAAYDVLKKSNPSPYMFFMQDND 300

Query: 301 FTLFGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELS 360
           FTLFGASPESSLKYDAT+RQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELS
Sbjct: 301 FTLFGASPESSLKYDATNRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELS 360

Query: 361 EHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRAC 420
           EHLMLVDLARNDLARICTPGSRYVADLTKVDRYS+VMHLVSRVVGELR DLD LHAYRAC
Sbjct: 361 EHLMLVDLARNDLARICTPGSRYVADLTKVDRYSFVMHLVSRVVGELRRDLDVLHAYRAC 420

Query: 421 MNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATV 480
           MNMGTLSGAPKVRAMQLIA AEG+RRGSYGGAVGYFTAHGDLDTCIVIRSA V++G+ATV
Sbjct: 421 MNMGTLSGAPKVRAMQLIAAAEGKRRGSYGGAVGYFTAHGDLDTCIVIRSAYVQDGVATV 480

Query: 481 QAGAGVVLDSVPQSEADETRNKARAVLRAIATAHHAQETF 520
           QAGAG+VLDSVPQSEADETRNKARAVLRAIA AHHA+E F
Sbjct: 481 QAGAGIVLDSVPQSEADETRNKARAVLRAIAQAHHAKEIF 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: 822
Number of extensions: 27
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 BWI76_RS11860 BWI76_RS11860 (anthranilate synthase component I)
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.23857.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.4e-261  854.6   0.0   1.5e-261  854.4   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11860  BWI76_RS11860 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11860  BWI76_RS11860 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  854.4   0.0  1.5e-261  1.5e-261       1     498 []      17     515 ..      17     515 .. 0.99

  Alignments for each domain:
  == domain 1  score: 854.4 bits;  conditional E-value: 1.5e-261
                               TIGR00565   1 yiadptalfeklcqdrpatlllesaeieskddlkslllvdaalkitclgdivtikalsnnGeallkkldaa 71 
                                             y+++ptalf+++c+ rpatlllesa+i+skddlkslllvd+al+it+lgd+vti+als+nG all+ ld+a
  lcl|FitnessBrowser__Koxy:BWI76_RS11860  17 YRENPTALFHQICGARPATLLLESADIDSKDDLKSLLLVDSALRITALGDTVTIHALSANGTALLELLDSA 87 
                                             99********************************************************************* PP

                               TIGR00565  72 lkalveavqsenalvlrflkvkklldedakllsasvfdalrllkslkqkpkep.ealllgGlfsydlvanf 141
                                             l+++++ ++++n++vl+f++v+ lldeda+l+s+svfda+rll++l ++p+++ ea+++gGlf+ydlva+f
  lcl|FitnessBrowser__Koxy:BWI76_RS11860  88 LPSGINNQRQPNSRVLTFPPVSALLDEDARLCSLSVFDAFRLLQELVTVPQDErEAMFFGGLFAYDLVAGF 158
                                             ***************************************************999***************** PP

                               TIGR00565 142 edlpqlkakndnvpdfifylaenlividhkeksveikaalfaer.eekqvaiakldlkeaqkskkadfvpk 211
                                             edlp l+ +  ++pd++fylae+l+vidh+ k+++i+a+lf +   ekq++ ++  ++++q+ +   ++p+
  lcl|FitnessBrowser__Koxy:BWI76_RS11860 159 EDLPSLESDT-ACPDYCFYLAETLLVIDHQTKNTRIQASLFTPLeSEKQRLLQRIAQLRQQLNEPPLPLPV 228
                                             ******9877.*******************************986899*********************** PP

                               TIGR00565 212 vsaasreveanlsdeefegvvkalkkeikkGeifqvvpsrrfslecpetlaayyqlkksnPsPymfylkde 282
                                               +a++++++++sdee++ vv+ ++++i++Geifqvvpsrrfsl+cp++laay +lkksnPsPymf+++d+
  lcl|FitnessBrowser__Koxy:BWI76_RS11860 229 TTVAEMRCDCDQSDEEYGAVVRKMQRAIRAGEIFQVVPSRRFSLPCPSPLAAYDVLKKSNPSPYMFFMQDN 299
                                             *********************************************************************** PP

                               TIGR00565 283 dfilfGasPesalkydaesrqleiyPiaGtrprGkdadGnidrdldsrlelelrldhkeraehlmlvdlar 353
                                             df+lfGasPes+lkyda++rq+eiyPiaGtrprG++adG++drdldsr+ele+r+dhke++ehlmlvdlar
  lcl|FitnessBrowser__Koxy:BWI76_RS11860 300 DFTLFGASPESSLKYDATNRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELSEHLMLVDLAR 370
                                             *********************************************************************** PP

                               TIGR00565 354 ndlarvcksgkryvaellkvdrysnvmhlvsrvvGelrkeldalhayracmnmGtlsGaPkikalqliyql 424
                                             ndlar+c++g+ryva+l+kvdrys+vmhlvsrvvGelr++ld lhayracmnmGtlsGaPk++a+qli+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS11860 371 NDLARICTPGSRYVADLTKVDRYSFVMHLVSRVVGELRRDLDVLHAYRACMNMGTLSGAPKVRAMQLIAAA 441
                                             *********************************************************************** PP

                               TIGR00565 425 enqrrgsyGGavGyltseGdldtcivirsalvkngiavvqaGaGvvldsvPqseadetrakaravlkairk 495
                                             e++rrgsyGGavGy+t++Gdldtcivirsa+v++g+a+vqaGaG+vldsvPqseadetr+karavl+ai++
  lcl|FitnessBrowser__Koxy:BWI76_RS11860 442 EGKRRGSYGGAVGYFTAHGDLDTCIVIRSAYVQDGVATVQAGAGIVLDSVPQSEADETRNKARAVLRAIAQ 512
                                             *********************************************************************** PP

                               TIGR00565 496 vsl 498
                                             +++
  lcl|FitnessBrowser__Koxy:BWI76_RS11860 513 AHH 515
                                             996 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.05
//
[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