Alignments for a candidate for trpE in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Acidithiobacillus ferrooxidans ATCC 23270

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_012537674.1 AFE_RS14870 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000021485.1:WP_012537674.1
          Length = 505

 Score =  602 bits (1551), Expect = e-176
 Identities = 316/489 (64%), Positives = 371/489 (75%), Gaps = 3/489 (0%)

Query: 6   FLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGLPC 65
           F  LA  GYNRIPLS E +AD DTPLS YLKL D P +YLLESVQGGEKWGRYSIIGLP 
Sbjct: 7   FEALARQGYNRIPLSREVIADLDTPLSAYLKLVDGPYAYLLESVQGGEKWGRYSIIGLPA 66

Query: 66  RTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQV-PTVPGLPRFDGGLVGYFG 124
           + +LRV    V + +DGVETER   ADPL ++  F+ R++V P      RF GGLVGYFG
Sbjct: 67  QQILRVTQGVVTVHVDGVETERATPADPLEWISVFRRRFRVAPLENADERFSGGLVGYFG 126

Query: 125 YDCVRYVEKRLA-TCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENAYER 183
           YD VR +E RLA + P PDPLG P+I L+V+D +++FDNL G +  +V ADP++  A+ER
Sbjct: 127 YDIVRSIEPRLARSTPLPDPLGLPEIQLLVADELLIFDNLRGTLRLLVHADPAQPEAWER 186

Query: 184 GQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGDCM 243
           G ARL EL +RLR+ + P     +     RE  F ASF+RE Y  AV  IK YI AGD M
Sbjct: 187 GAARLRELQQRLRESVPPSSP-PVSTRHVREEDFTASFSREGYMAAVRTIKAYIGAGDVM 245

Query: 244 QVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLVTV 303
           QVVPSQR+S    A P+DLYRALR  NP+PYM++ + GD H+VGSSPE+LVRVE+  VTV
Sbjct: 246 QVVPSQRLSTPLTAHPLDLYRALRGINPSPYMFYVDLGDTHLVGSSPEILVRVEEDQVTV 305

Query: 304 RPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMV 363
           RPIAGTRPRG     D ALEQ+LL+D KE AEHLMLIDL RNDVGR++D G+V++T+   
Sbjct: 306 RPIAGTRPRGKTPAEDEALEQELLADPKERAEHLMLIDLARNDVGRIADTGSVRLTDSFG 365

Query: 364 IERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVY 423
           IERYS+VMHIVS VTG+LR  L AMDALRA  PAGT+SGAPKIRAMEII E+EPV RGVY
Sbjct: 366 IERYSHVMHIVSQVTGRLRPELDAMDALRATFPAGTVSGAPKIRAMEIIREVEPVARGVY 425

Query: 424 GGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMFRA 483
            GAVGY  WNGNMDT IAIRTAVIK+G LH+QAGGGIVADS PA EWEET+NKRRAMFRA
Sbjct: 426 AGAVGYWGWNGNMDTCIAIRTAVIKDGMLHIQAGGGIVADSEPAAEWEETMNKRRAMFRA 485

Query: 484 VALAEQSVE 492
           VALAE  ++
Sbjct: 486 VALAENGLD 494


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: 772
Number of extensions: 35
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: 492
Length of database: 505
Length adjustment: 34
Effective length of query: 458
Effective length of database: 471
Effective search space:   215718
Effective search space used:   215718
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_012537674.1 AFE_RS14870 (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.1468212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-178  577.8   0.0   1.1e-177  577.6   0.0    1.0  1  NCBI__GCF_000021485.1:WP_012537674.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021485.1:WP_012537674.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.6   0.0  1.1e-177  1.1e-177       2     454 ..      27     486 ..      26     487 .. 0.94

  Alignments for each domain:
  == domain 1  score: 577.6 bits;  conditional E-value: 1.1e-177
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ieedelkel 72 
                                           d  tp+s+ylkl   ++ +llEsv+ +e++gRyS+igl  ++ +++++g +v++++d+ e++  + +d+l+ +
  NCBI__GCF_000021485.1:WP_012537674.1  27 DLDTPLSAYLKLVDGPYAYLLESVQGGEKWGRYSIIGLPAQQILRVTQG-VVTVHVDGVETEraTPADPLEWI 98 
                                           778**********99************************9999999999.44444444333334799999999 PP

                             TIGR00564  73 rklleka.eesedeldeplsggavGylgydtvrlveklke..ea.edelelpdlllllvetvivfDhvekkvi 141
                                             + +++     ++ de +sgg+vGy+gyd+vr++e+  +  ++ +d+l lp++ ll+ +++++fD+ + ++ 
  NCBI__GCF_000021485.1:WP_012537674.1  99 SVFRRRFrVAPLENADERFSGGLVGYFGYDIVRSIEPRLArsTPlPDPLGLPEIQLLVADELLIFDNLRGTLR 171
                                           9999998656678899********************9766443369**************************9 PP

                             TIGR00564 142 lienarteaersaeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeyeekvakakeyikaGd 211
                                           l+ +a  ++ + a+e  aarl+el ++l++++ ++   v++ + ++e+ft+++++e y+++v+++k yi aGd
  NCBI__GCF_000021485.1:WP_012537674.1 172 LLVHADPAQPE-AWERGAARLRELQQRLRESVPPSsppVSTRHVREEDFTASFSREGYMAAVRTIKAYIGAGD 243
                                           99999677666.9****************9998877778899999999************************* PP

                             TIGR00564 212 ifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGa 284
                                           ++qvv+Sqrl+++++a+p++lYr+LR +NPSpy++y+dl d++lvgsSPE+lv+v++++v++rPiAGtr+RG+
  NCBI__GCF_000021485.1:WP_012537674.1 244 VMQVVPSQRLSTPLTAHPLDLYRALRGINPSPYMFYVDLGDTHLVGSSPEILVRVEEDQVTVRPIAGTRPRGK 316
                                           ************************************************************************* PP

                             TIGR00564 285 tkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdelta 357
                                           t++eDeale+eLlad+KerAEHlmL+DLaRND+g++a++gsv+ ++++ ie+yshvmHivS+V+G+l++el+a
  NCBI__GCF_000021485.1:WP_012537674.1 317 TPAEDEALEQELLADPKERAEHLMLIDLARNDVGRIADTGSVRLTDSFGIERYSHVMHIVSQVTGRLRPELDA 389
                                           ************************************************************************* PP

                             TIGR00564 358 vDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGi 430
                                           +Dalra++PaGT+sGAPK+rAme+i e+E++ Rg+Y+Gavgy++ +g++dt+iaiRt+v+kdg++++qAg+Gi
  NCBI__GCF_000021485.1:WP_012537674.1 390 MDALRATFPAGTVSGAPKIRAMEIIREVEPVARGVYAGAVGYWGWNGNMDTCIAIRTAVIKDGMLHIQAGGGI 462
                                           ************************************************************************* PP

                             TIGR00564 431 VaDSdpeaEyeEtlnKakallrai 454
                                           VaDS+p aE+eEt+nK +a+ ra+
  NCBI__GCF_000021485.1:WP_012537674.1 463 VADSEPAAEWEETMNKRRAMFRAV 486
                                           ********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (505 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: 00:00:00.00
# Mc/sec: 29.46
//
[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