Alignments for a candidate for trpD_2 in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Klebsiella michiganensis M5al

Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate BWI76_RS11855 BWI76_RS11855 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase

Query= SwissProt::P00904
         (531 letters)



>FitnessBrowser__Koxy:BWI76_RS11855
          Length = 531

 Score = 1001 bits (2588), Expect = 0.0
 Identities = 502/531 (94%), Positives = 518/531 (97%)

Query: 1   MADILLLDNIDSFTYNLADQLRSNGHNVVIYRNHIPAQTLIERLATMSNPVLMLSPGPGV 60
           MADILLLDNIDSFTYNLADQLRSNGHNVVIYRN +PAQ LIER+ TM NPVLMLSPGPG 
Sbjct: 1   MADILLLDNIDSFTYNLADQLRSNGHNVVIYRNSVPAQALIERIGTMKNPVLMLSPGPGT 60

Query: 61  PSEAGCMPELLTRLRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF 120
           PSEAGCMPELL R+RGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF
Sbjct: 61  PSEAGCMPELLIRMRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF 120

Query: 121 AGLTNPLPVARYHSLVGSNIPAGLTINAHFNGMVMAVRHDADRVCGFQFHPESILTTQGA 180
           AGL+NPLPVARYHSLVGSNIPAGLTINAHFNGMVMAVRHDADRVCGFQFHPESILTTQGA
Sbjct: 121 AGLSNPLPVARYHSLVGSNIPAGLTINAHFNGMVMAVRHDADRVCGFQFHPESILTTQGA 180

Query: 181 RLLEQTLAWAQQKLEPANTLQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALV 240
           RLLEQTLAWA QKLE  NTLQPILEKLYQA+TLSQQESHQLFSAVVRGE+KPEQLAAALV
Sbjct: 181 RLLEQTLAWALQKLEQTNTLQPILEKLYQAETLSQQESHQLFSAVVRGEVKPEQLAAALV 240

Query: 241 SMKIRGEHPNEIAGAATALLENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAAC 300
           SMK+RGEHP EIAGAATALLENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAAC
Sbjct: 241 SMKVRGEHPQEIAGAATALLENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAAC 300

Query: 301 GLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHA 360
           GLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHA
Sbjct: 301 GLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHA 360

Query: 361 MPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGG 420
           MPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGG
Sbjct: 361 MPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGG 420

Query: 421 MDEVSLHAPTIVAELHDGEIKSYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKG 480
           MDEVSLHAPT+VAEL++GEIKSYQLTA DFGLTPYHQEQLAGGTPEENRDILTRLLQGKG
Sbjct: 421 MDEVSLHAPTVVAELNNGEIKSYQLTAADFGLTPYHQEQLAGGTPEENRDILTRLLQGKG 480

Query: 481 DAAHEAAVAANVAMLMRLHGHEDLQANAQTVLEVLRSGSAYDRVTALAARG 531
           +AAHEAAVAANVAMLMRLHG+EDL+ANAQ V++VL SG+AYDRVTALAARG
Sbjct: 481 EAAHEAAVAANVAMLMRLHGYEDLKANAQQVIDVLHSGAAYDRVTALAARG 531


Lambda     K      H
   0.318    0.134    0.388 

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: 1070
Number of extensions: 23
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: 531
Length of database: 531
Length adjustment: 35
Effective length of query: 496
Effective length of database: 496
Effective search space:   246016
Effective search space used:   246016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS11855 BWI76_RS11855 (bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# 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/TIGR01245.hmm
# target sequence database:        /tmp/gapView.14622.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.2e-132  426.4   0.1   5.2e-132  426.1   0.1    1.1  1  lcl|FitnessBrowser__Koxy:BWI76_RS11855  BWI76_RS11855 bifunctional gluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11855  BWI76_RS11855 bifunctional glutamine amidotransferase/anthranilate phosphorib
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.1   0.1  5.2e-132  5.2e-132       1     328 [.     204     528 ..     204     530 .. 0.99

  Alignments for each domain:
  == domain 1  score: 426.1 bits;  conditional E-value: 5.2e-132
                               TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseel 71 
                                             lekl++ ++Ls++e++ql++++++ge++++q+aA+lv ++v+ge+++eiag+a+al+e+a  +++ +++ +
  lcl|FitnessBrowser__Koxy:BWI76_RS11855 204 LEKLYQAETLSQQESHQLFSAVVRGEVKPEQLAAALVSMKVRGEHPQEIAGAATALLENAAPFPR-PDYLF 273
                                             689************************************************************99.7**** PP

                               TIGR01245  72 vDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevg 142
                                             +DivGTGGDg+++iNiSTasa+vaaa+G+kvaKhGnrsvssksGs+D+L a+g+nl+++++k++++l+e+g
  lcl|FitnessBrowser__Koxy:BWI76_RS11855 274 ADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRQALDELG 344
                                             *********************************************************************** PP

                               TIGR01245 143 igFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralv 213
                                             ++FlfAPkyh+++++++pvR++L++rt+fN+LGPL+nPa+++l+++Gvys++lv  +ae+l+ lg++ra v
  lcl|FitnessBrowser__Koxy:BWI76_RS11855 345 VCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAV 415
                                             *********************************************************************** PP

                               TIGR01245 214 vhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakr 284
                                             vh+ +g+DE+sl+++t vael++gei++y+l+++dfgl+++++e+l+gg++een ++l+++l+gk++ a++
  lcl|FitnessBrowser__Koxy:BWI76_RS11855 416 VHS-GGMDEVSLHAPTVVAELNNGEIKSYQLTAADFGLTPYHQEQLAGGTPEENRDILTRLLQGKGEAAHE 485
                                             ***.******************************************************************* PP

                               TIGR01245 285 divvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                             ++v++N+a++++++g++ dlk++++++ ++++sg+a++ +++l+
  lcl|FitnessBrowser__Koxy:BWI76_RS11855 486 AAVAANVAMLMRLHGYE-DLKANAQQVIDVLHSGAAYDRVTALA 528
                                             ***************99.********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (531 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.21
//
[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