Alignments for a candidate for trpE in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Haloechinothrix alba DSM 45207

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_089300784.1 CHB84_RS07580 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_900188115.1:WP_089300784.1
          Length = 546

 Score =  382 bits (981), Expect = e-110
 Identities = 227/507 (44%), Positives = 306/507 (60%), Gaps = 26/507 (5%)

Query: 2   NREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLA-DQPNSYLLESVQGGEKWGRYSM 60
           +REEF  LA      IP+    LAD +TP+ +Y KLA D+P ++L ES + GE W R+S 
Sbjct: 15  SREEFRALARER-RVIPVVRTVLADAETPIGLYRKLAADRPGTFLFESAEHGESWSRWSF 73

Query: 61  IGLPSRTVMRVHGYHVSIL-HDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGL 119
           +G+ S   + VH    + L H  V + S    +PL+ +    +      +P +P   GG+
Sbjct: 74  VGVRSPAALTVHDGEATWLGHPPVGLPSGG--NPLSALREAVEELHSEPLPDMPPLTGGM 131

Query: 120 VGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAI---VLVDPA 176
           VGY GYD VR++E+        D L +P+++++++  +  +D+  G +  I   V  D +
Sbjct: 132 VGYIGYDAVRWLERL--PEHARDDLRIPELIMLLATDLAAYDHHEGTVTLIANAVNWDAS 189

Query: 177 EEQ---AFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRI 233
            E+   A++   ARL  +   L QP TP        P    P+F    T EDY +A+ R 
Sbjct: 190 PERVDAAYDDSVARLDEMSAALAQP-TPPTAATFDRPA---PQFHRRRTPEDYHDAIRRA 245

Query: 234 KEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMY------FFNFGD---FH 284
            E + AG+  Q+VPSQR  +   A  +D+YR LR  NP+PYMY      F + GD   F 
Sbjct: 246 VEAVHAGEAFQIVPSQRFEMATGADALDVYRVLRTSNPSPYMYLLRLDGFDSNGDQIAFD 305

Query: 285 VVGSSPEVLVRVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGR 344
           +VGSSPE LV V D   T  PIAGTR R    + D  L  DLL+DDKE AEHLML+DLGR
Sbjct: 306 IVGSSPESLVTVRDGRATTHPIAGTRWRAEDPDEDAMLAKDLLADDKERAEHLMLVDLGR 365

Query: 345 NDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAP 404
           ND+GRV   G+V + +   IERYS+VMHIVS V G+L  G TA+DA+ A  PAGTL+GAP
Sbjct: 366 NDLGRVCKPGTVHVVDSFSIERYSHVMHIVSTVTGELDAGATAVDAVAACFPAGTLTGAP 425

Query: 405 KIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADS 464
           K+RAME+IDELEP +RG+YGG VGY  + G+ DTAIAIRTA++ DG  +VQAGGG+VADS
Sbjct: 426 KVRAMELIDELEPTRRGLYGGVVGYLDFAGDADTAIAIRTALMRDGVAYVQAGGGVVADS 485

Query: 465 VPALEWEETINKRRAMFRAVALAEQTS 491
            P  E  E++NK R +  AVA AE  S
Sbjct: 486 SPEYEDNESLNKARTVLAAVAAAETMS 512


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: 766
Number of extensions: 39
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: 546
Length adjustment: 35
Effective length of query: 458
Effective length of database: 511
Effective search space:   234038
Effective search space used:   234038
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_089300784.1 CHB84_RS07580 (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.12012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-169  549.4   0.0   4.4e-169  549.2   0.0    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089300784.1  CHB84_RS07580 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089300784.1  CHB84_RS07580 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.2   0.0  4.4e-169  4.4e-169       1     453 [.      37     504 ..      37     506 .. 0.96

  Alignments for each domain:
  == domain 1  score: 549.2 bits;  conditional E-value: 4.4e-169
                                 TIGR00564   1 adtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieede 68 
                                               ad++tpi +y+kla  r+ +fl+Es+e++e+++R+S++g+++ + ++++dg+a++l +        +++
  lcl|NCBI__GCF_900188115.1:WP_089300784.1  37 ADAETPIGLYRKLAAdRPGTFLFESAEHGESWSRWSFVGVRSPAALTVHDGEATWLGHPPVGLPSGGNP 105
                                               599************88***************************************9777777799*** PP

                                 TIGR00564  69 lkelrkllekaeesedeld..eplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDh 135
                                               l++lr+ +e+++  ++ l+  +pl+gg+vGy+gyd vr +e+l+e+a+d+l++p+l++ll ++++++Dh
  lcl|NCBI__GCF_900188115.1:WP_089300784.1 106 LSALREAVEELH--SEPLPdmPPLTGGMVGYIGYDAVRWLERLPEHARDDLRIPELIMLLATDLAAYDH 172
                                               **********64..445665689********************************************** PP

                                 TIGR00564 136 vekkvilienarteaers......aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyee 198
                                                e +v+li+na + +  s      a+++  arl+e+ a l +++ +++ +  + + +f+ + + e+y++
  lcl|NCBI__GCF_900188115.1:WP_089300784.1 173 HEGTVTLIANAVNWD-ASpervdaAYDDSVARLDEMSAALAQPTPPTAATFDRPAPQFHRRRTPEDYHD 240
                                               *********996654.4446888999*******************999999999999************ PP

                                 TIGR00564 199 kvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldled.........felvgs 258
                                               ++++a e+++aG+ fq+v+Sqr+e+ + a+++++Yr+LRt+NPSpy+y l l++         f +vgs
  lcl|NCBI__GCF_900188115.1:WP_089300784.1 241 AIRRAVEAVHAGEAFQIVPSQRFEMATGADALDVYRVLRTSNPSPYMYLLRLDGfdsngdqiaFDIVGS 309
                                               *****************************************************9999999*99****** PP

                                 TIGR00564 259 SPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsve 327
                                               SPE+lv+v++ r +t+PiAGtr R ++++eD++l+++Llad KerAEHlmLvDL+RND+g+v+k+g+v+
  lcl|NCBI__GCF_900188115.1:WP_089300784.1 310 SPESLVTVRDGRATTHPIAGTRWRAEDPDEDAMLAKDLLADDKERAEHLMLVDLGRNDLGRVCKPGTVH 378
                                               ********************************************************************* PP

                                 TIGR00564 328 vkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGa 396
                                               v ++++ie+yshvmHivS+V+Gel  ++tavDa+ a++PaGTl+GAPKvrAmelidelE+++Rg+YgG+
  lcl|NCBI__GCF_900188115.1:WP_089300784.1 379 VVDSFSIERYSHVMHIVSTVTGELDAGATAVDAVAACFPAGTLTGAPKVRAMELIDELEPTRRGLYGGV 447
                                               ********************************************************************* PP

                                 TIGR00564 397 vgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallra 453
                                               vgyl+f+gd dtaiaiRt++++dgvayvqAg+G+VaDS+pe E +E+lnKa+++l a
  lcl|NCBI__GCF_900188115.1:WP_089300784.1 448 VGYLDFAGDADTAIAIRTALMRDGVAYVQAGGGVVADSSPEYEDNESLNKARTVLAA 504
                                               ****************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (546 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: 14.36
//
[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