Alignments for a candidate for trpE in Desulfogranum mediterraneum DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Desulfogranum mediterraneum DSM 13871

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_028585452.1 G494_RS0116875 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000429965.1:WP_028585452.1
          Length = 494

 Score =  417 bits (1071), Expect = e-121
 Identities = 232/482 (48%), Positives = 312/482 (64%), Gaps = 17/482 (3%)

Query: 17  IPLACETLADFDTPLSIYLKLADQ-PNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYH 75
           +P+  + +AD DTPL+I+ K+A Q P+++L ES++GGEKWGRYS IG+ S          
Sbjct: 19  VPVHRKIVADLDTPLTIFAKVAGQDPHAFLFESMEGGEKWGRYSFIGMDSLVTFESVKDQ 78

Query: 76  VSILHDGVEVESHDVED---PLAFVESFKDRYKVADIPGLPRFNGGLVGYFGYDCVRYVE 132
           V   + G + E+  VE+   PL  +      ++V+D PGLPRF GG VG+ GYD +R++E
Sbjct: 79  VRWTYPGRKEENR-VENGAQPLDELRQLLASFEVSDAPGLPRFYGGAVGFLGYDMIRFIE 137

Query: 133 KRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE----EQAFEQGQARL 188
               +     P G PD   MV   V++ D++   +  +  +   +    EQ ++QG  R+
Sbjct: 138 D---IPDRHAPSGFPDSSFMVPGVVLIHDSVEQTLTIVCNLWQQDGEDAEQLYQQGCQRI 194

Query: 189 QGLLETLRQPITPRRGLDLSGPQAAEPE-FRSSYTREDYENAVGRIKEYILAGDCMQVVP 247
           + L+  + QP+ P    DL    A EP  F S+  +E +   V + KEYILAGD +QVV 
Sbjct: 195 EELVAAIHQPVPP----DLIRQHAVEPHVFSSNMEQESFAAMVEQAKEYILAGDIIQVVL 250

Query: 248 SQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIA 307
           SQR     +  P  LYRALR  NP+PY+++   G+  ++GSSPE+LVR+E+  + +RPIA
Sbjct: 251 SQRFHARSQLNPFTLYRALRHINPSPYLFYLRCGELILIGSSPEILVRLENEAIELRPIA 310

Query: 308 GTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERY 367
           GTR RGAT E D ALE++LL+D KE AEHLML+DLGRNDVGRV+  GSV + + +VIERY
Sbjct: 311 GTRKRGATPEEDLALEEELLADPKERAEHLMLVDLGRNDVGRVARAGSVEVKDLLVIERY 370

Query: 368 SNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAV 427
           S+VMHIVS V G+L  G    D + A  PAGT+SGAPKIRAMEIIDELE   RG Y GAV
Sbjct: 371 SHVMHIVSGVEGKLEPGKDQFDVMEACFPAGTVSGAPKIRAMEIIDELETEGRGPYAGAV 430

Query: 428 GYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALA 487
           GYF ++GNMD  I IRT ++ +  L +QAG GIVADS PA E+EETINK   + RAV LA
Sbjct: 431 GYFGFSGNMDFCITIRTFILQEDNLWIQAGAGIVADSDPASEYEETINKSMGLRRAVELA 490

Query: 488 EQ 489
           E+
Sbjct: 491 EK 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: 638
Number of extensions: 36
Number of successful extensions: 6
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_028585452.1 G494_RS0116875 (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.2444029.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-175  569.6   0.0   3.3e-175  569.4   0.0    1.0  1  NCBI__GCF_000429965.1:WP_028585452.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000429965.1:WP_028585452.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  569.4   0.0  3.3e-175  3.3e-175       2     454 ..      28     487 ..      27     488 .. 0.94

  Alignments for each domain:
  == domain 1  score: 569.4 bits;  conditional E-value: 3.3e-175
                             TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak...ieedelk 70 
                                           d  tp++++ k+a  +++ fl+Es+e +e++gRyS+ig+++  +++  ++++ +     +e++   + +++l+
  NCBI__GCF_000429965.1:WP_028585452.1  28 DLDTPLTIFAKVAGqDPHAFLFESMEGGEKWGRYSFIGMDSLVTFESVKDQVRWTYPGRKEENrveNGAQPLD 100
                                           778**********978******************************999988776543333333347789*** PP

                             TIGR00564  71 elrklleka.eesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvil 142
                                           elr+ll+++  ++ ++l+  ++ggavG+lgyd++r++e++++++  +  +pd  +++   v+++D ve+++++
  NCBI__GCF_000429965.1:WP_028585452.1 101 ELRQLLASFeVSDAPGLPR-FYGGAVGFLGYDMIRFIEDIPDRHA-PSGFPDSSFMVPGVVLIHDSVEQTLTI 171
                                           *********4444566665.*********************9874.679************************ PP

                             TIGR00564 143 ienarteaers...aeeeaaarleellaelqkeleka.vkaleekkesftsnvekeeyeekvakakeyikaGd 211
                                           + n  ++++++    +++  +r+eel+a +++++ ++ ++++  +++ f+sn+e+e++++ v++akeyi aGd
  NCBI__GCF_000429965.1:WP_028585452.1 172 VCNLWQQDGEDaeqLYQQGCQRIEELVAAIHQPVPPDlIRQHAVEPHVFSSNMEQESFAAMVEQAKEYILAGD 244
                                           **9999998886666788999***************977777788888************************* PP

                             TIGR00564 212 ifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGa 284
                                           i+qvvlSqr++a+ +++pf lYr+LR++NPSpyl+yl + ++ l+gsSPE+lv+++++ +e rPiAGtrkRGa
  NCBI__GCF_000429965.1:WP_028585452.1 245 IIQVVLSQRFHARSQLNPFTLYRALRHINPSPYLFYLRCGELILIGSSPEILVRLENEAIELRPIAGTRKRGA 317
                                           ********************************************************999************** PP

                             TIGR00564 285 tkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdelta 357
                                           t+eeD aleeeLlad+KerAEHlmLvDL+RND+g+va++gsvevk+ll ie+yshvmHivS VeG+l++++++
  NCBI__GCF_000429965.1:WP_028585452.1 318 TPEEDLALEEELLADPKERAEHLMLVDLGRNDVGRVARAGSVEVKDLLVIERYSHVMHIVSGVEGKLEPGKDQ 390
                                           ************************************************************************* PP

                             TIGR00564 358 vDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGi 430
                                           +D++ a++PaGT+sGAPK+rAme+idelE+e Rg+Y+Gavgy++f g++d++i+iRt +l+++ + +qAgaGi
  NCBI__GCF_000429965.1:WP_028585452.1 391 FDVMEACFPAGTVSGAPKIRAMEIIDELETEGRGPYAGAVGYFGFSGNMDFCITIRTFILQEDNLWIQAGAGI 463
                                           ************************************************************************* PP

                             TIGR00564 431 VaDSdpeaEyeEtlnKakallrai 454
                                           VaDSdp +EyeEt+nK+++l ra+
  NCBI__GCF_000429965.1:WP_028585452.1 464 VADSDPASEYEETINKSMGLRRAV 487
                                           *******************99987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.00
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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