Alignments for a candidate for trpE in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Shewanella sp. ANA-3

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate 7024328 Shewana3_1520 anthranilate synthase component I (RefSeq)

Query= SwissProt::P00895
         (520 letters)



>FitnessBrowser__ANA3:7024328
          Length = 563

 Score =  501 bits (1289), Expect = e-146
 Identities = 275/507 (54%), Positives = 350/507 (69%), Gaps = 12/507 (2%)

Query: 16  AYRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALRITALGDTVTIQALSG 75
           AY  +P  L+  +  D P T+LLESA+IDSK++LKS+++  +AL I   G  +   ALS 
Sbjct: 35  AYHSDPLRLYQHITQDVPHTMLLESAEIDSKENLKSMVMTHAALMIRCDGYRLRFSALSD 94

Query: 76  NGEALLALLDN---ALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCSLSVFDAFRLLQN 132
           NG +LLA ++    A  +  + ++  +  V+     + L DEDARL S S  D  RL   
Sbjct: 95  NGVSLLAPIEQFFIARSSQTQCQRDGHNLVVTLQKDTELKDEDARLKSTSPLDGLRLFVK 154

Query: 133 LLNVPKEER-EAMFFGGLFSYDLVAGFEDLPQL-SAENNCPDFCFYLAETLMVIDHQKKS 190
            ++  +    E +F GG+ SYDL+   E LP+  +  N+CPD+ FYLAETL++IDH++K 
Sbjct: 155 HIDCGQTPAFEDLFLGGVLSYDLIDTVEPLPEAPNGANDCPDYLFYLAETLILIDHKQKH 214

Query: 191 TRIQASLFAPNEEEKQRLTARLNELRQQ-------LTEAAPPLPVVSVPHMRCECNQSDE 243
             I    F+   E+   +T  L E  +        L ++A P P +       + N SD+
Sbjct: 215 AEIITHNFSEGTEQHLEVTQALAERAENISAQCEALAKSATPAPALVGITATEQVNVSDD 274

Query: 244 EFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDNDFTL 303
           +F   V  L++ I AG+IFQVVPSR FSLPCP  L AY  L+ +NPSPYMF+ +  DFTL
Sbjct: 275 DFKQTVIDLKEHIIAGDIFQVVPSRSFSLPCPDTLGAYRALRLTNPSPYMFYFRGYDFTL 334

Query: 304 FGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELSEHL 363
           FGASPES+LKY+A++ Q+E+YPIAGTR RG+ A G +D DLDSRIELE+R D KELSEHL
Sbjct: 335 FGASPESALKYEASNNQVEVYPIAGTRKRGKTASGEIDFDLDSRIELELRLDKKELSEHL 394

Query: 364 MLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRACMNM 423
           MLVDLARND+ARI   GSR VA+L KVDRYS+VMHLVSRV G+LR DLDALHAY+ACMNM
Sbjct: 395 MLVDLARNDIARISQSGSRKVAELLKVDRYSHVMHLVSRVTGQLRQDLDALHAYQACMNM 454

Query: 424 GTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATVQAG 483
           GTL GAPKVRA QL+ +AE  RRGSYGGAVGY  A GD+DTCIVIRSA V+NG+A +QAG
Sbjct: 455 GTLVGAPKVRASQLVRQAEKTRRGSYGGAVGYLNALGDMDTCIVIRSAFVKNGVAHIQAG 514

Query: 484 AGVVLDSVPQSEADETRNKARAVLRAI 510
           AGVV DS PQSEADETR KA+AV+ AI
Sbjct: 515 AGVVFDSDPQSEADETRQKAQAVISAI 541


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: 633
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: 563
Length adjustment: 35
Effective length of query: 485
Effective length of database: 528
Effective search space:   256080
Effective search space used:   256080
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 7024328 Shewana3_1520 (anthranilate synthase component I (RefSeq))
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.25933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.2e-212  692.3   0.1   2.7e-212  692.0   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7024328  Shewana3_1520 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024328  Shewana3_1520 anthranilate synthase component I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.0   0.1  2.7e-212  2.7e-212       1     494 [.      36     542 ..      36     545 .. 0.93

  Alignments for each domain:
  == domain 1  score: 692.0 bits;  conditional E-value: 2.7e-212
                         TIGR00565   1 yiadptalfeklcqdrpatlllesaeieskddlkslllvdaalkitclgdivtikalsnnGeallkkldaalkal.. 75 
                                       y++dp+ l+++++qd p+t+llesaei+sk++lks+++ +aal i c g  + + als+nG +ll+ +++++ a   
  lcl|FitnessBrowser__ANA3:7024328  36 YHSDPLRLYQHITQDVPHTMLLESAEIDSKENLKSMVMTHAALMIRCDGYRLRFSALSDNGVSLLAPIEQFFIARss 112
                                       8899********************************************************************99943 PP

                         TIGR00565  76 .veavqsenalvlrflkvkklldedakllsasvfdalrllkslkqkpkep..ealllgGlfsydlvanfedlpqlka 149
                                         ++++  ++lv++ +k  +l+deda+l s+s++d+lrl+ +  +  ++p  e l+lgG++sydl+ + e+lp+   
  lcl|FitnessBrowser__ANA3:7024328 113 qTQCQRDGHNLVVTLQKDTELKDEDARLKSTSPLDGLRLFVKHIDCGQTPafEDLFLGGVLSYDLIDTVEPLPEAPN 189
                                       233344456899****************************99999999998889*********************** PP

                         TIGR00565 150 kndnvpdfifylaenlividhkeksveikaalfaereek..qvai...akldl...keaqkskkadfvpkvsaasre 218
                                         +++pd+ fylae+li+idhk+k++ei +  f+e  e+  +v++   ++ +    +  +++k+a + p     +  
  lcl|FitnessBrowser__ANA3:7024328 190 GANDCPDYLFYLAETLILIDHKQKHAEIITHNFSEGTEQhlEVTQalaERAENisaQCEALAKSATPAPALVGITAT 266
                                       *9*******************************99755511233311033222000223455666677777777778 PP

                         TIGR00565 219 veanlsdeefegvvkalkkeikkGeifqvvpsrrfslecpetlaayyqlkksnPsPymfylkdedfilfGasPesal 295
                                        ++n+sd++f++ v  lk++i +G+ifqvvpsr+fsl+cp+tl ay  l+ +nPsPymfy++  df+lfGasPesal
  lcl|FitnessBrowser__ANA3:7024328 267 EQVNVSDDDFKQTVIDLKEHIIAGDIFQVVPSRSFSLPCPDTLGAYRALRLTNPSPYMFYFRGYDFTLFGASPESAL 343
                                       899************************************************************************** PP

                         TIGR00565 296 kydaesrqleiyPiaGtrprGkdadGnidrdldsrlelelrldhkeraehlmlvdlarndlarvcksgkryvaellk 372
                                       ky+a ++q+e+yPiaGtr rGk a G+id dldsr+elelrld ke++ehlmlvdlarnd+ar+++sg+r+vaellk
  lcl|FitnessBrowser__ANA3:7024328 344 KYEASNNQVEVYPIAGTRKRGKTASGEIDFDLDSRIELELRLDKKELSEHLMLVDLARNDIARISQSGSRKVAELLK 420
                                       ***************************************************************************** PP

                         TIGR00565 373 vdrysnvmhlvsrvvGelrkeldalhayracmnmGtlsGaPkikalqliyqlenqrrgsyGGavGyltseGdldtci 449
                                       vdrys+vmhlvsrv G+lr++ldalhay+acmnmGtl GaPk++a ql+ q+e+ rrgsyGGavGyl++ Gd+dtci
  lcl|FitnessBrowser__ANA3:7024328 421 VDRYSHVMHLVSRVTGQLRQDLDALHAYQACMNMGTLVGAPKVRASQLVRQAEKTRRGSYGGAVGYLNALGDMDTCI 497
                                       ***************************************************************************** PP

                         TIGR00565 450 virsalvkngiavvqaGaGvvldsvPqseadetrakaravlkair 494
                                       virsa+vkng+a++qaGaGvv+ds+Pqseadetr+ka+av+ ai+
  lcl|FitnessBrowser__ANA3:7024328 498 VIRSAFVKNGVAHIQAGAGVVFDSDPQSEADETRQKAQAVISAIK 542
                                       ********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (498 nodes)
Target sequences:                          1  (563 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: 10.27
//
[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