Alignments for a candidate for trpE in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Halomonas desiderata SP1

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_086511648.1 BZY95_RS19935 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_002151265.1:WP_086511648.1
          Length = 494

 Score =  626 bits (1614), Expect = 0.0
 Identities = 319/499 (63%), Positives = 382/499 (76%), Gaps = 20/499 (4%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M  E F  LA  G+NRIP+  E LAD DTPLS YLKLAD+P ++LLESVQGGEKWGRYS+
Sbjct: 1   MTPERFRALADAGFNRIPVTREVLADLDTPLSTYLKLADEPWTFLLESVQGGEKWGRYSI 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLPS   + V G+ +S +  G  +E  +V DPLA++E+F+ R++V ++   PRF+GGLV
Sbjct: 61  IGLPSHERIEVRGFTISHVRQGECIERVEVADPLAWIEAFQGRFRVPNLDDQPRFDGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180
           GYFGYD +RY+E RL     PDPLGVPDILLMV D +VVFDNL+G++      DPA   A
Sbjct: 121 GYFGYDTIRYIEPRLRGVEKPDPLGVPDILLMVCDELVVFDNLSGRLTLWTHADPAAADA 180

Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEP----------EFRSSYTREDYENAV 230
           F    ARL+ L   LR           SG QAA P           F S +T   ++ AV
Sbjct: 181 FATAVARLESLERRLRS----------SGVQAASPGTGRSAVEEGHFTSGFTEAGFKAAV 230

Query: 231 GRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSP 290
            +IKEY+LAGD MQ VPSQRMSI ++A+P+DLYRALR  NP+PYM+FFN GD HVVGSSP
Sbjct: 231 EKIKEYVLAGDVMQCVPSQRMSIPYRASPLDLYRALRSLNPSPYMFFFNLGDHHVVGSSP 290

Query: 291 EVLVRVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRV 350
           E+L R+ED  VTVRPIAGTR RG TEE DRALE +LL+D KEIAEHLMLIDLGRNDVGR+
Sbjct: 291 EILTRLEDGEVTVRPIAGTRVRGKTEEEDRALEAELLADPKEIAEHLMLIDLGRNDVGRI 350

Query: 351 SSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAME 410
           S TGSV++T++M +ERYS+VMHIVSNV G+L+ GL+AMD LRA  PAGTLSGAPKIRAME
Sbjct: 351 SETGSVQVTDQMAVERYSHVMHIVSNVTGRLKPGLSAMDVLRATFPAGTLSGAPKIRAME 410

Query: 411 IIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEW 470
           IIDELEPVKRG+Y GAVGY +W+GNMDTAIAIRTAVI DGELHVQAG G+VADSVP +EW
Sbjct: 411 IIDELEPVKRGIYSGAVGYLSWHGNMDTAIAIRTAVIKDGELHVQAGAGVVADSVPEMEW 470

Query: 471 EETINKRRAMFRAVALAEQ 489
           +ET+NK RA+FRAVA+AE+
Sbjct: 471 QETLNKGRAIFRAVAMAEK 489


Lambda     K      H
   0.320    0.138    0.403 

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: 788
Number of extensions: 35
Number of successful extensions: 2
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: 493
Length of database: 494
Length adjustment: 34
Effective length of query: 459
Effective length of database: 460
Effective search space:   211140
Effective search space used:   211140
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 WP_086511648.1 BZY95_RS19935 (anthranilate synthase component I)
to HMM TIGR00564 (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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.14157.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-175  570.5   0.0   1.7e-175  570.4   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511648.1  BZY95_RS19935 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511648.1  BZY95_RS19935 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.4   0.0  1.7e-175  1.7e-175       2     454 ..      26     484 ..      25     485 .. 0.93

  Alignments for each domain:
  == domain 1  score: 570.4 bits;  conditional E-value: 1.7e-175
                                 TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedel 69 
                                               d  tp+s ylkla ++ +fllEsv+ +e++gRyS+igl ++ +i++++ ++ ++++ +  ++ +++d+l
  lcl|NCBI__GCF_002151265.1:WP_086511648.1  26 DLDTPLSTYLKLADEPWTFLLESVQGGEKWGRYSIIGLPSHERIEVRGFTISHVRQGECIERvEVADPL 94 
                                               778********************************************9766555544444444667777 PP

                                 TIGR00564  70 kelrkllekaeesedeld..eplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfD 134
                                                 ++++  +  ++ ++ld  + + gg+vGy+gydt+r++e+  +  e++d+l +pd+ll+++++++vfD
  lcl|NCBI__GCF_002151265.1:WP_086511648.1  95 AWIEAFQGR--FRVPNLDdqPRFDGGLVGYFGYDTIRYIEPRLRgvEKPDPLGVPDILLMVCDELVVFD 161
                                               777766666..55777776578******************99887566********************* PP

                                 TIGR00564 135 hvekkvilienarteaersaeeeaaarleellaelqkeleka....vkaleekkesftsnvekeeyeek 199
                                               + + +++l ++a  +a   a++ a arle+l ++l+++  +a    + +   ++ +fts ++++ ++++
  lcl|NCBI__GCF_002151265.1:WP_086511648.1 162 NLSGRLTLWTHADPAAAD-AFATAVARLESLERRLRSSGVQAaspgTGRSAVEEGHFTSGFTEAGFKAA 229
                                               **********99777666.9***************999887754334455555666************* PP

                                 TIGR00564 200 vakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkg 268
                                               v+k+key+ aGd++q v+Sqr++ + +a+p++lYr+LR+ NPSpy+++++l d ++vgsSPE+l ++++
  lcl|NCBI__GCF_002151265.1:WP_086511648.1 230 VEKIKEYVLAGDVMQCVPSQRMSIPYRASPLDLYRALRSLNPSPYMFFFNLGDHHVVGSSPEILTRLED 298
                                               ********************************************************************* PP

                                 TIGR00564 269 krvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkieky 337
                                                +v++rPiAGtr RG+t+eeD+ale+eLlad+Ke AEHlmL+DL+RND+g+++++gsv+v++ + +e+y
  lcl|NCBI__GCF_002151265.1:WP_086511648.1 299 GEVTVRPIAGTRVRGKTEEEDRALEAELLADPKEIAEHLMLIDLGRNDVGRISETGSVQVTDQMAVERY 367
                                               ********************************************************************* PP

                                 TIGR00564 338 shvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdv 406
                                               shvmHivS+V+G+lk++l+a+D+lra++PaGTlsGAPK+rAme+idelE++kRgiY+Gavgyls +g++
  lcl|NCBI__GCF_002151265.1:WP_086511648.1 368 SHVMHIVSNVTGRLKPGLSAMDVLRATFPAGTLSGAPKIRAMEIIDELEPVKRGIYSGAVGYLSWHGNM 436
                                               ********************************************************************* PP

                                 TIGR00564 407 dtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               dtaiaiRt+v+kdg ++vqAgaG+VaDS+pe E++EtlnK +a  ra+
  lcl|NCBI__GCF_002151265.1:WP_086511648.1 437 DTAIAIRTAVIKDGELHVQAGAGVVADSVPEMEWQETLNKGRAIFRAV 484
                                               *******************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (494 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.66
//
[ok]

This GapMind analysis is from Apr 10 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