Alignments for a candidate for trpE in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Phaeobacter inhibens BS107

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate GFF1663 PGA1_c16860 anthranilate synthase component 1

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Phaeo:GFF1663
          Length = 503

 Score =  420 bits (1080), Expect = e-122
 Identities = 239/494 (48%), Positives = 319/494 (64%), Gaps = 21/494 (4%)

Query: 4   EEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLAD-QPNSYLLESVQGGEKWGRYSMIG 62
           + F +    G N++ +     AD DTP+S+ LKL   Q ++++LESV GGE  GRYS+IG
Sbjct: 8   DTFAKAYEAGENQV-VYTRLAADLDTPVSLMLKLTGAQKDAFILESVTGGEVRGRYSIIG 66

Query: 63  LPSRTVMRVHGYHVSILHDG-VEVESHDVED--PLAFVESFKDRYKVADIPG-LPRFNGG 118
           +    V R HG   ++      + ++ +  D  PL  +       K+ D+P  LP+   G
Sbjct: 67  MKPDLVWRCHGERAALNRSARFDADAFEPLDGNPLDCLRDLIAESKI-DLPDDLPQAAAG 125

Query: 119 LVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPA-- 176
           L GY GYD +R VE    V  NPDPLG+PD L++    + V D + G+   + +V PA  
Sbjct: 126 LFGYLGYDMIRLVEHLPDV--NPDPLGLPDALMLRPSVIAVLDGVKGE---VTVVSPAWA 180

Query: 177 -----EEQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVG 231
                 + A+ Q   R+   +  L + + P    DL       P   S++T++ Y  AV 
Sbjct: 181 SDGQSAKAAYAQAAERVMDAVRDLERAM-PAESRDLGDADEVAPPV-SNFTKDGYMAAVE 238

Query: 232 RIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPE 291
           + K+YI AGD  QVVP+QR +  F+  P  LYR+LR  NP+P+M++FNFG F VVG+SPE
Sbjct: 239 KAKDYIRAGDIFQVVPAQRWTQTFRQPPFALYRSLRRTNPSPFMFYFNFGGFQVVGASPE 298

Query: 292 VLVRVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVS 351
           +LVRV    VT+RPIAGTRPRGAT E D+ALE DLL+D KE+AEHLML+DLGRND GRV+
Sbjct: 299 ILVRVFGQEVTIRPIAGTRPRGATPEEDKALELDLLADKKELAEHLMLLDLGRNDTGRVA 358

Query: 352 STGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEI 411
             G+VR TEK +IERYS+VMHIVSNV G+L E   A+DA  A +PAGT+SGAPK+RAMEI
Sbjct: 359 KIGTVRPTEKFIIERYSHVMHIVSNVVGELAEDKDALDAFFAGMPAGTVSGAPKVRAMEI 418

Query: 412 IDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWE 471
           IDELEP KRGVYGG VGYF+  G+MD  IA+RTA++ D  L++QAGGG+V DS P  E+ 
Sbjct: 419 IDELEPEKRGVYGGGVGYFSAGGDMDMCIALRTAIVKDQNLYIQAGGGVVYDSDPEAEYM 478

Query: 472 ETINKRRAMFRAVA 485
           ET++K  A+ RA A
Sbjct: 479 ETVHKSNAIRRAAA 492


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: 697
Number of extensions: 30
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: 493
Length of database: 503
Length adjustment: 34
Effective length of query: 459
Effective length of database: 469
Effective search space:   215271
Effective search space used:   215271
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 GFF1663 PGA1_c16860 (anthranilate synthase component 1)
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.5369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.2e-173  561.5   0.0   9.6e-173  561.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1663  PGA1_c16860 anthranilate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1663  PGA1_c16860 anthranilate synthase component 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.3   0.0  9.6e-173  9.6e-173       2     454 ..      29     491 ..      28     492 .. 0.91

  Alignments for each domain:
  == domain 1  score: 561.3 bits;  conditional E-value: 9.6e-173
                          TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak....ieedelkel 72 
                                        d  tp+s++lkl+  +k  f+lEsv+ +e +gRyS+ig++p+l++++++++a l + +  +a      ++++l+ l
  lcl|FitnessBrowser__Phaeo:GFF1663  29 DLDTPVSLMLKLTGaQKDAFILESVTGGEVRGRYSIIGMKPDLVWRCHGERAALNRSARFDADafepLDGNPLDCL 104
                                        778***********99********************************99554443332222234579******** PP

                          TIGR00564  73 rkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvilienart 148
                                        r+l+++ +++ ++  ++ ++g++Gylgyd++rlve+l++ ++d+l lpd+l+l  + ++v D v+ +v++++ a  
  lcl|FitnessBrowser__Phaeo:GFF1663 105 RDLIAESKIDLPDDLPQAAAGLFGYLGYDMIRLVEHLPDVNPDPLGLPDALMLRPSVIAVLDGVKGEVTVVSPAWA 180
                                        ******8766554446689******************************************************999 PP

                          TIGR00564 149 eaers...aeeeaaarleellaelqkelekavkaleekkes...ftsnvekeeyeekvakakeyikaGdifqvvlS 218
                                        ++++s   a+++aa+r+ + +++l++++  + + l ++  +     sn++k+ y+++v+kak+yi+aGdifqvv++
  lcl|FitnessBrowser__Phaeo:GFF1663 181 SDGQSakaAYAQAAERVMDAVRDLERAMPAESRDLGDAD-EvapPVSNFTKDGYMAAVEKAKDYIRAGDIFQVVPA 255
                                        999985555555666666666666666654433222222.23457899999************************* PP

                          TIGR00564 219 qrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealee 294
                                        qr ++ ++++pf+lYr+LR++NPSp+++y+++ +f++vg+SPE+lv+v g++v++rPiAGtr+RGat+eeD+ale 
  lcl|FitnessBrowser__Phaeo:GFF1663 256 QRWTQTFRQPPFALYRSLRRTNPSPFMFYFNFGGFQVVGASPEILVRVFGQEVTIRPIAGTRPRGATPEEDKALEL 331
                                        **************************************************************************** PP

                          TIGR00564 295 eLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTl 370
                                        +Llad+Ke AEHlmL+DL+RND g+vak+g+v+ +e + ie+yshvmHivS+V+Gel+++++a+Da+ a +PaGT+
  lcl|FitnessBrowser__Phaeo:GFF1663 332 DLLADKKELAEHLMLLDLGRNDTGRVAKIGTVRPTEKFIIERYSHVMHIVSNVVGELAEDKDALDAFFAGMPAGTV 407
                                        **************************************************************************** PP

                          TIGR00564 371 sGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnK 446
                                        sGAPKvrAme+idelE+ekRg+YgG+vgy+s+ gd+d++ia+Rt+++kd+ +y+qAg+G+V+DSdpeaEy Et++K
  lcl|FitnessBrowser__Phaeo:GFF1663 408 SGAPKVRAMEIIDELEPEKRGVYGGGVGYFSAGGDMDMCIALRTAIVKDQNLYIQAGGGVVYDSDPEAEYMETVHK 483
                                        **************************************************************************** PP

                          TIGR00564 447 akallrai 454
                                        ++a  ra+
  lcl|FitnessBrowser__Phaeo:GFF1663 484 SNAIRRAA 491
                                        ***99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (503 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.34
//
[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