Alignments for a candidate for trpE in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Shewanella oneidensis MR-1

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate 202141 SO3019 anthranilate synthase component I (NCBI ptt file)

Query= SwissProt::P00895
         (520 letters)



>FitnessBrowser__MR1:202141
          Length = 574

 Score =  497 bits (1280), Expect = e-145
 Identities = 274/512 (53%), Positives = 351/512 (68%), Gaps = 18/512 (3%)

Query: 17  YRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALRITALGDTVTIQALSGN 76
           Y  +P  L+  +  D P T+LLESA+I+SK++LKS+++  +AL I   G  +   AL+ N
Sbjct: 36  YHSDPLRLYQHITEDAPHTMLLESAEINSKENLKSMVMTHAALMIRCDGYRLRFSALTDN 95

Query: 77  GEALLALLDN---ALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCSLSVFDAFRLLQNL 133
           G +LL  ++    A     + +++    V+     + L DEDARL S S  D  RL    
Sbjct: 96  GASLLTPIEQFFMARSCHTQCQRNGQHLVVTLQKDTELKDEDARLKSTSPLDGLRLFVKH 155

Query: 134 LNV-------PKEEREAMFFGGLFSYDLVAGFEDLPQL-SAENNCPDFCFYLAETLMVID 185
           ++         K   E +F GG+ SYDL+   E LP+  +  N+CPD+ FYLAETL++ID
Sbjct: 156 IDCGAHTDSQSKPAFEDLFLGGVLSYDLIDTVEPLPEAPNGANDCPDYLFYLAETLILID 215

Query: 186 HQKKSTRIQASLFAPNEEEK----QRLTARLNELRQQ---LTEAAPPLPVVSVPHMRCEC 238
           H++K   I    F+ + E+     Q L  R+  +R Q   L ++A P P +       + 
Sbjct: 216 HKQKQAEIITHNFSESAEQHSEVTQALAERVENIRAQCEALAKSATPAPALVGITATEQV 275

Query: 239 NQSDEEFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQD 298
           N SDE F   V  L++ I AG+IFQVVPSR FSLPCP+ L AY  L+ +NPSPYMF+ + 
Sbjct: 276 NVSDEAFKQTVIDLKEHIIAGDIFQVVPSRSFSLPCPNTLGAYRALRLTNPSPYMFYFRG 335

Query: 299 NDFTLFGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKE 358
           NDFTLFGASPES+LK+D+++ Q+E+YPIAGTR RG+ A G +D DLDSRIELE+R D KE
Sbjct: 336 NDFTLFGASPESALKFDSSNNQVEVYPIAGTRKRGKTASGEIDFDLDSRIELELRLDKKE 395

Query: 359 LSEHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYR 418
           LSEHLMLVDLARND+ARI   GSR VA+L KVDRYS+VMHLVSRV G+LR DLDALHAY+
Sbjct: 396 LSEHLMLVDLARNDIARISQSGSRKVAELLKVDRYSHVMHLVSRVTGQLRQDLDALHAYQ 455

Query: 419 ACMNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIA 478
           ACMNMGTL GAPKVRA QL+ +AE  RRGSYGGAVGY  A GD+DTCIVIRSA V++G+A
Sbjct: 456 ACMNMGTLVGAPKVRASQLVRQAEKTRRGSYGGAVGYLNALGDMDTCIVIRSAFVKDGVA 515

Query: 479 TVQAGAGVVLDSVPQSEADETRNKARAVLRAI 510
            +QAGAGVV DS PQSEADETR KA+AV+ AI
Sbjct: 516 HIQAGAGVVFDSDPQSEADETRQKAQAVISAI 547


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: 642
Number of extensions: 24
Number of successful extensions: 5
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: 574
Length adjustment: 36
Effective length of query: 484
Effective length of database: 538
Effective search space:   260392
Effective search space used:   260392
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 202141 SO3019 (anthranilate synthase component I (NCBI ptt file))
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.14832.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.4e-210  683.7   0.2     1e-209  683.5   0.2    1.0  1  lcl|FitnessBrowser__MR1:202141  SO3019 anthranilate synthase com


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202141  SO3019 anthranilate synthase component I (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.5   0.2    1e-209    1e-209       1     494 [.      36     548 ..      36     551 .. 0.91

  Alignments for each domain:
  == domain 1  score: 683.5 bits;  conditional E-value: 1e-209
                       TIGR00565   1 yiadptalfeklcqdrpatlllesaeieskddlkslllvdaalkitclgdivtikalsnnGeallkkldaalkal...v 76 
                                     y++dp+ l++++++d p+t+llesaei+sk++lks+++ +aal i c g  + + al++nG +ll  +++++ a     
  lcl|FitnessBrowser__MR1:202141  36 YHSDPLRLYQHITEDAPHTMLLESAEINSKENLKSMVMTHAALMIRCDGYRLRFSALTDNGASLLTPIEQFFMARschT 114
                                     8899********************************************************************9986445 PP

                       TIGR00565  77 eavqsenalvlrflkvkklldedakllsasvfdalrll.ksl....kqkpkep...ealllgGlfsydlvanfedlpql 147
                                     +++++ + lv++ +k  +l+deda+l s+s++d+lrl+ k +    ++ ++ +   e l+lgG++sydl+ + e+lp+ 
  lcl|FitnessBrowser__MR1:202141 115 QCQRNGQHLVVTLQKDTELKDEDARLKSTSPLDGLRLFvKHIdcgaHTDSQSKpafEDLFLGGVLSYDLIDTVEPLPEA 193
                                     5566677899**************************7624442222233333324678********************* PP

                       TIGR00565 148 kakndnvpdfifylaenlividhkeksveikaalfaer..eekqvaia...kldlkeaq...kskkadfvpkvsaasre 218
                                         +++pd+ fylae+li+idhk+k++ei +  f+e   ++ +v++a   + +  +aq   ++k+a + p     +  
  lcl|FitnessBrowser__MR1:202141 194 PNGANDCPDYLFYLAETLILIDHKQKQAEIITHNFSESaeQHSEVTQAlaeRVENIRAQceaLAKSATPAPALVGITAT 272
                                     ***9*******************************99732233444441114444443311155667777888778888 PP

                       TIGR00565 219 veanlsdeefegvvkalkkeikkGeifqvvpsrrfslecpetlaayyqlkksnPsPymfylkdedfilfGasPesalky 297
                                      ++n+sde f++ v  lk++i +G+ifqvvpsr+fsl+cp+tl ay  l+ +nPsPymfy++ +df+lfGasPesalk+
  lcl|FitnessBrowser__MR1:202141 273 EQVNVSDEAFKQTVIDLKEHIIAGDIFQVVPSRSFSLPCPNTLGAYRALRLTNPSPYMFYFRGNDFTLFGASPESALKF 351
                                     899**************************************************************************** PP

                       TIGR00565 298 daesrqleiyPiaGtrprGkdadGnidrdldsrlelelrldhkeraehlmlvdlarndlarvcksgkryvaellkvdry 376
                                     d+ ++q+e+yPiaGtr rGk a G+id dldsr+elelrld ke++ehlmlvdlarnd+ar+++sg+r+vaellkvdry
  lcl|FitnessBrowser__MR1:202141 352 DSSNNQVEVYPIAGTRKRGKTASGEIDFDLDSRIELELRLDKKELSEHLMLVDLARNDIARISQSGSRKVAELLKVDRY 430
                                     ******************************************************************************* PP

                       TIGR00565 377 snvmhlvsrvvGelrkeldalhayracmnmGtlsGaPkikalqliyqlenqrrgsyGGavGyltseGdldtcivirsal 455
                                     s+vmhlvsrv G+lr++ldalhay+acmnmGtl GaPk++a ql+ q+e+ rrgsyGGavGyl++ Gd+dtcivirsa+
  lcl|FitnessBrowser__MR1:202141 431 SHVMHLVSRVTGQLRQDLDALHAYQACMNMGTLVGAPKVRASQLVRQAEKTRRGSYGGAVGYLNALGDMDTCIVIRSAF 509
                                     ******************************************************************************* PP

                       TIGR00565 456 vkngiavvqaGaGvvldsvPqseadetrakaravlkair 494
                                     vk+g+a++qaGaGvv+ds+Pqseadetr+ka+av+ ai+
  lcl|FitnessBrowser__MR1:202141 510 VKDGVAHIQAGAGVVFDSDPQSEADETRQKAQAVISAIK 548
                                     **************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (498 nodes)
Target sequences:                          1  (574 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.38
//
[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