Alignments for a candidate for trpE in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Thioalkalivibrio denitrificans ALJD

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_077277377.1 B1C78_RS01525 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_002000365.1:WP_077277377.1
          Length = 489

 Score =  616 bits (1588), Expect = 0.0
 Identities = 316/488 (64%), Positives = 376/488 (77%), Gaps = 3/488 (0%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M+ E+F  L   GYNRIPL  E LAD DTPLS+YLKLA AP SYL ESVQGGEKWGRYS 
Sbjct: 1   MSPEQFDELIRQGYNRIPLVREVLADLDTPLSVYLKLAAAPYSYLFESVQGGEKWGRYSF 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           +GLP RTV++V   +V +   G   E  + ADPLA+VE+F+AR +VP + GLPRF GGLV
Sbjct: 61  VGLPARTVVKVRGRRVTVEEGGAVVEDTEVADPLAWVEDFQARQRVPDIEGLPRFTGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYFGYD +RY+E RLA    PDPLG PDILLMVSD VVV+DNLAG+++ +V A P  E  
Sbjct: 121 GYFGYDTIRYIEPRLAGTEKPDPLGVPDILLMVSDEVVVYDNLAGRLYLVVHARP--ETG 178

Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAG 240
               QARLEEL  RL  P+        +A +  E  F + FT + ++ AV R KDYI+ G
Sbjct: 179 LAAAQARLEELRGRLAAPVAAPAATG-DARKVHESDFVSGFTEDGFKAAVARCKDYIVEG 237

Query: 241 DCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGL 300
           D MQVV SQR+SI F A P++LYRALR  NP+PYM+F +  D  VVGSSPE+LVR+ED +
Sbjct: 238 DVMQVVLSQRLSIPFAAPPVNLYRALRSLNPSPYMFFLDLDDHQVVGSSPEILVRLEDDI 297

Query: 301 VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTE 360
           VTVRPIAGTRPRG  E  D ALE +LL+D KE AEHLMLIDLGRND GRVS+ G+V++TE
Sbjct: 298 VTVRPIAGTRPRGATEAEDHALEAELLADPKERAEHLMLIDLGRNDAGRVSETGSVQLTE 357

Query: 361 KMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420
           +MV+ERYS+VMHIVSNVTG+L+ G+SAMD LRA  PAGT+SGAPKIRAMEIIDELEPVKR
Sbjct: 358 QMVVERYSHVMHIVSNVTGRLKAGMSAMDVLRATFPAGTVSGAPKIRAMEIIDELEPVKR 417

Query: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           G+Y GAVGYL+W GNMDTAIAIRTAVIK+G+LH+QAG GIV DS+P  EW ET+NK RA+
Sbjct: 418 GIYAGAVGYLSWAGNMDTAIAIRTAVIKDGQLHIQAGAGIVHDSIPDNEWAETMNKGRAI 477

Query: 481 FRAVALAE 488
           FRAVA+ E
Sbjct: 478 FRAVAMVE 485


Lambda     K      H
   0.321    0.139    0.408 

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: 733
Number of extensions: 29
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: 492
Length of database: 489
Length adjustment: 34
Effective length of query: 458
Effective length of database: 455
Effective search space:   208390
Effective search space used:   208390
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_077277377.1 B1C78_RS01525 (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.3519297.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-178  580.5   0.0   1.6e-178  580.3   0.0    1.0  1  NCBI__GCF_002000365.1:WP_077277377.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002000365.1:WP_077277377.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.3   0.0  1.6e-178  1.6e-178       2     454 ..      26     481 ..      25     482 .. 0.93

  Alignments for each domain:
  == domain 1  score: 580.3 bits;  conditional E-value: 1.6e-178
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelrk 74 
                                           d  tp+svylkla  ++s+l+Esv+ +e++gRyS++gl  ++++k+++    ++++++  a +e+ e+ +  +
  NCBI__GCF_002000365.1:WP_077277377.1  26 DLDTPLSVYLKLAAAPYSYLFESVQGGEKWGRYSFVGLPARTVVKVRGR---RVTVEEGGAVVEDTEVADPLA 95 
                                           778*******************************************987...555556666667777777888 PP

                             TIGR00564  75 lleka..eesedeld..eplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivfDhvekkvi 141
                                           ++e +  +++ ++++  + ++gg+vGy+gydt+r++e+  +  e++d+l +pd+ll++ ++v+v+D+ + +++
  NCBI__GCF_002000365.1:WP_077277377.1  96 WVEDFqaRQRVPDIEglPRFTGGLVGYFGYDTIRYIEPRLAgtEKPDPLGVPDILLMVSDEVVVYDNLAGRLY 168
                                           8887755566777778888******************98775466**************************** PP

                             TIGR00564 142 lienarteaersaeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeyeekvakakeyikaGd 211
                                           l+ +ar e++    ++a+arleel  +l  +++      +a + ++ +f s ++++ ++++va+ k+yi +Gd
  NCBI__GCF_002000365.1:WP_077277377.1 169 LVVHARPETGL---AAAQARLEELRGRLAAPVAAPaatGDARKVHESDFVSGFTEDGFKAAVARCKDYIVEGD 238
                                           *****888655...799************9998773223344455566************************* PP

                             TIGR00564 212 ifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGa 284
                                           ++qvvlSqrl+ ++ a+p++lYr+LR+ NPSpy+++ldl+d ++vgsSPE+lv+++++ v++rPiAGtr+RGa
  NCBI__GCF_002000365.1:WP_077277377.1 239 VMQVVLSQRLSIPFAAPPVNLYRALRSLNPSPYMFFLDLDDHQVVGSSPEILVRLEDDIVTVRPIAGTRPRGA 311
                                           ********************************************************999************** PP

                             TIGR00564 285 tkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdelta 357
                                           t++eD+ale+eLlad+KerAEHlmL+DL+RND g+v+++gsv+ +e + +e+yshvmHivS+V+G+lk +++a
  NCBI__GCF_002000365.1:WP_077277377.1 312 TEAEDHALEAELLADPKERAEHLMLIDLGRNDAGRVSETGSVQLTEQMVVERYSHVMHIVSNVTGRLKAGMSA 384
                                           ************************************************************************* PP

                             TIGR00564 358 vDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGi 430
                                           +D+lra++PaGT+sGAPK+rAme+idelE++kRgiY+Gavgyls +g++dtaiaiRt+v+kdg++++qAgaGi
  NCBI__GCF_002000365.1:WP_077277377.1 385 MDVLRATFPAGTVSGAPKIRAMEIIDELEPVKRGIYAGAVGYLSWAGNMDTAIAIRTAVIKDGQLHIQAGAGI 457
                                           ************************************************************************* PP

                             TIGR00564 431 VaDSdpeaEyeEtlnKakallrai 454
                                           V DS p++E+ Et+nK +a  ra+
  NCBI__GCF_002000365.1:WP_077277377.1 458 VHDSIPDNEWAETMNKGRAIFRAV 481
                                           *******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (489 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: 17.01
//
[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