Alignments for a candidate for trpE in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Magnetospirillum magneticum AMB-1

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate AMB_RS09175 AMB_RS09175 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__Magneto:AMB_RS09175
          Length = 506

 Score =  407 bits (1046), Expect = e-118
 Identities = 231/472 (48%), Positives = 306/472 (64%), Gaps = 16/472 (3%)

Query: 24  LADFDTPLSIYLKLAD-QPNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHVSILHDG 82
           +AD +TP+S ++KLA  QPN++LLESV+GG   GRYS++G+    + +  G    I  + 
Sbjct: 27  VADLETPVSAFMKLAGGQPNAFLLESVEGGAVRGRYSILGMRPDLLWKCVGNEAWINRNA 86

Query: 83  VEVESHDVEDPLAFVESFKD--RYKVADI-----PGLPRFNGGLVGYFGYDCVRYVEKRL 135
               S  +  P+A      D  R  VA+      P LP  + GL+GY  YD VR  EK  
Sbjct: 87  RSKTSEFLPCPVAAKSGALDSLRALVAECGIETPPHLPPMSAGLIGYMSYDMVRLAEKL- 145

Query: 136 GVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE----EQAFEQGQARLQGL 191
               NPDP+ VPD + M    + VFDN+ G + A+  V P      + A++    RL+ +
Sbjct: 146 -PDANPDPIKVPDGIFMRPTIMAVFDNVNGTLTAVAPVWPRAGMDAQAAWDLAWERLEHI 204

Query: 192 LETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQRM 251
           +E+L  P+ P   L     +  +P    S + E Y   V + +EYI AGD  QVV SQR+
Sbjct: 205 VESLESPL-PHTYLGFPRDEH-QPIPVPSVSPEHYCRMVEKAQEYIAAGDIFQVVLSQRL 262

Query: 252 SIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGTRP 311
           ++ F+  P  LYR+LR  NP+P+++F + G+F +VGSSPE+LVR+ D+ VT+RPIAGTR 
Sbjct: 263 AVPFRLPPFSLYRSLRRLNPSPFLFFLDLGEFQLVGSSPEILVRLRDDKVTIRPIAGTRR 322

Query: 312 RGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSNVM 371
           RG T   D  L  DLL+D KE+AEHLML+DLGRNDVGRV++ G+V +T+KM +E YS+VM
Sbjct: 323 RGKTPAEDEELAADLLADPKELAEHLMLLDLGRNDVGRVAAIGTVEVTKKMTVEYYSHVM 382

Query: 372 HIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFA 431
           HIVSNV G++REG  AMDAL A  PAGT SGAPKIRAMEIIDELE  +R  Y GA+GYF 
Sbjct: 383 HIVSNVEGKIREGCDAMDALMAGFPAGTTSGAPKIRAMEIIDELETERRSFYAGAIGYFD 442

Query: 432 WNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRA 483
            NGNMDT IA+RT ++ DG ++VQAG GIVADSVP  E EE +NK RA+ RA
Sbjct: 443 GNGNMDTCIALRTTLVKDGTMYVQAGAGIVADSVPLSEHEECMNKARALVRA 494


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: 688
Number of extensions: 34
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: 506
Length adjustment: 34
Effective length of query: 459
Effective length of database: 472
Effective search space:   216648
Effective search space used:   216648
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 AMB_RS09175 AMB_RS09175 (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.4038930.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.9e-177  576.7   0.0   2.2e-177  576.5   0.0    1.0  1  FitnessBrowser__Magneto:AMB_RS09175  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Magneto:AMB_RS09175  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.5   0.0  2.2e-177  2.2e-177       1     454 [.      28     495 ..      28     496 .. 0.95

  Alignments for each domain:
  == domain 1  score: 576.5 bits;  conditional E-value: 2.2e-177
                            TIGR00564   1 adtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak........ie 65 
                                          ad +tp+s++ kla  +++ fllEsve ++ +gRyS++g++p+l +k+ +++a + +++ ++++         +
  FitnessBrowser__Magneto:AMB_RS09175  28 ADLETPVSAFMKLAGgQPNAFLLESVEGGAVRGRYSILGMRPDLLWKCVGNEAWINRNARSKTSeflpcpvaAK 101
                                          5889***********99********************************9966555444443335999999889 PP

                            TIGR00564  66 edelkelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekk 139
                                          + +l++lr+l++++ ++++   +p+s+g++Gy++yd+vrl ekl+++++d++++pd +++  + ++vfD+v+ +
  FitnessBrowser__Magneto:AMB_RS09175 102 SGALDSLRALVAECGIETPPHLPPMSAGLIGYMSYDMVRLAEKLPDANPDPIKVPDGIFMRPTIMAVFDNVNGT 175
                                          99************7777777788************************************************** PP

                            TIGR00564 140 vilienarteaers...aeeeaaarleellaelqkeleka.vkaleekkes.ftsnvekeeyeekvakakeyik 208
                                          ++ ++ +  +a+ +   a++ a +rle+++++l+++l ++   ++ +++++   ++v+ e+y   v+ka+eyi+
  FitnessBrowser__Magneto:AMB_RS09175 176 LTAVAPVWPRAGMDaqaAWDLAWERLEHIVESLESPLPHTyLGFPRDEHQPiPVPSVSPEHYCRMVEKAQEYIA 249
                                          *****999999988777888999**************9986455555444456799****************** PP

                            TIGR00564 209 aGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkR 282
                                          aGdifqvvlSqrl+++++++pf+lYr+LR+ NPSp+l++ldl +f+lvgsSPE+lv++++++v++rPiAGtr+R
  FitnessBrowser__Magneto:AMB_RS09175 250 AGDIFQVVLSQRLAVPFRLPPFSLYRSLRRLNPSPFLFFLDLGEFQLVGSSPEILVRLRDDKVTIRPIAGTRRR 323
                                          ************************************************************************** PP

                            TIGR00564 283 GatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdelt 356
                                          G+t++eDe l+++Llad+Ke AEHlmL+DL+RND+g+va +g+vev++ +++e yshvmHivS+VeG+++++ +
  FitnessBrowser__Magneto:AMB_RS09175 324 GKTPAEDEELAADLLADPKELAEHLMLLDLGRNDVGRVAAIGTVEVTKKMTVEYYSHVMHIVSNVEGKIREGCD 397
                                          ************************************************************************** PP

                            TIGR00564 357 avDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGi 430
                                          a+Dal+a +PaGT sGAPK+rAme+idelE+e+R +Y+Ga+gy++ +g++dt+ia+Rt ++kdg++yvqAgaGi
  FitnessBrowser__Magneto:AMB_RS09175 398 AMDALMAGFPAGTTSGAPKIRAMEIIDELETERRSFYAGAIGYFDGNGNMDTCIALRTTLVKDGTMYVQAGAGI 471
                                          ************************************************************************** PP

                            TIGR00564 431 VaDSdpeaEyeEtlnKakallrai 454
                                          VaDS+p +E+eE++nKa+al+ra+
  FitnessBrowser__Magneto:AMB_RS09175 472 VADSVPLSEHEECMNKARALVRAA 495
                                          *********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (506 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: 00:00:00.01
# Mc/sec: 14.46
//
[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