GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Paraburkholderia bryophila 376MFSha3.1

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate H281DRAFT_05715 H281DRAFT_05715 anthranilate synthase, component I

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__Burk376:H281DRAFT_05715
          Length = 497

 Score =  536 bits (1380), Expect = e-157
 Identities = 277/500 (55%), Positives = 358/500 (71%), Gaps = 14/500 (2%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLA----DAPNSYLLESVQGGEKWG 56
           M   EF  LA +G+NRIPL  E LAD +TPLS+YLKLA    +  NS+LLESV GGE++G
Sbjct: 1   MTELEFQSLANEGFNRIPLIAEALADLETPLSLYLKLAQPERNGANSFLLESVVGGERFG 60

Query: 57  RYSIIGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFD 116
           RYS IGLP RT+LR  +    +  DG   E  +  DPL F+++F++R++V   PGLPRF 
Sbjct: 61  RYSFIGLPARTLLRTRNGVSEVVRDGKVVETHE-GDPLEFIQQFQSRFKVAQRPGLPRFA 119

Query: 117 GGLVGYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPS 176
           GGL GYFGYD VRY+EK+LA     D L  PDI L++++ V V DNLAGK++ ++ ADP+
Sbjct: 120 GGLAGYFGYDAVRYIEKKLAHSAPKDDLNLPDIQLLLTEEVAVIDNLAGKLYLVIYADPT 179

Query: 177 EENAYERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDY 236
           +  AY + + RL EL +RLR  + P     + +A  R   +R  F ++DY  AV + K+Y
Sbjct: 180 QPEAYTKAKQRLRELRQRLRATVEP----PVTSASVRTETYR-EFAKDDYLAAVRKAKEY 234

Query: 237 ILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRV 296
           I AG+ MQV   QR++  ++  P+ LYRALR  NP+PYMY++NFGDFHVVG+SPE+LVR 
Sbjct: 235 IAAGELMQVQVGQRLTKPYRDNPLSLYRALRSLNPSPYMYYYNFGDFHVVGASPEILVRQ 294

Query: 297 E----DGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSD 352
           E    D +VT+RP+AGTRPRG   E D  L  +LL+D KEIAEH+MLIDL RNDVGR++ 
Sbjct: 295 EKRGEDRIVTIRPLAGTRPRGNTPERDAELATELLNDPKEIAEHVMLIDLARNDVGRIAQ 354

Query: 353 IGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEII 412
           IG+V VT+KMVIE+YS+V HIVS+V G+L+ G +  D LRA  PAGTLSGAPK+RAME+I
Sbjct: 355 IGSVVVTDKMVIEKYSHVQHIVSSVEGKLKPGTTNFDVLRATFPAGTLSGAPKVRAMELI 414

Query: 413 DELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEE 472
           DELEPVKRG+YGGAVGYL++ G MD AI IRT VI NG L+VQA  G+VADSVP  EW+E
Sbjct: 415 DELEPVKRGLYGGAVGYLSFTGEMDLAITIRTGVIANGNLYVQAAAGVVADSVPESEWQE 474

Query: 473 TINKRRAMFRAVALAEQSVE 492
           T NK RA+ RA    +  ++
Sbjct: 475 TENKARAVLRAAEQVQDGLD 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: 632
Number of extensions: 29
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: 497
Length adjustment: 34
Effective length of query: 458
Effective length of database: 463
Effective search space:   212054
Effective search space used:   212054
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 H281DRAFT_05715 H281DRAFT_05715 (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.32233.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.6e-170  551.5   0.0   9.9e-170  551.3   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05715  H281DRAFT_05715 anthranilate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05715  H281DRAFT_05715 anthranilate synthase, component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.3   0.0  9.9e-170  9.9e-170       1     454 [.      25     486 ..      25     487 .. 0.94

  Alignments for each domain:
  == domain 1  score: 551.3 bits;  conditional E-value: 9.9e-170
                                    TIGR00564   1 adtltpisvylklak.r...kesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeea 62 
                                                  ad +tp+s+ylkla+ +   ++sfllEsv  +e+ gRyS+igl  ++ +++++g + ++  d++  
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715  25 ADLETPLSLYLKLAQpErngANSFLLESVVGGERFGRYSFIGLPARTLLRTRNG-VSEVVRDGKVV 89 
                                                  5889**********97568899*********************99999999987.55555565555 PP

                                    TIGR00564  63 k.ieedelkelrklleka.eesedeldeplsggavGylgydtvrlveklke..eaedelelpdlll 124
                                                  + +e+d+l+ ++++ +++   ++++l+  ++gg+ Gy+gyd vr++ek+ +  +++d+l+lpd+ l
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715  90 EtHEGDPLEFIQQFQSRFkVAQRPGLPR-FAGGLAGYFGYDAVRYIEKKLAhsAPKDDLNLPDIQL 154
                                                  55899*************6667788887.******************99774345*********** PP

                                    TIGR00564 125 llvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsn 190
                                                  ll+e+v+v D+ + k++l+ +a  ++ + a+++a++rl+el ++l+ ++e+ v+    ++e++  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 155 LLTEEVAVIDNLAGKLYLVIYADPTQPE-AYTKAKQRLRELRQRLRATVEPPVTSASVRTETY-RE 218
                                                  **********************888777.9********************9998777777666.99 PP

                                    TIGR00564 191 vekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelv 256
                                                  + k++y ++v+kakeyi+aG+++qv++ qrl+++ + +p++lYr+LR+ NPSpy+yy ++ df++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 219 FAKDDYLAAVRKAKEYIAAGELMQVQVGQRLTKPYRDNPLSLYRALRSLNPSPYMYYYNFGDFHVV 284
                                                  ****************************************************************** PP

                                    TIGR00564 257 gsSPEllvkvk...gkr.vetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDig 318
                                                  g+SPE+lv+ +   ++r v++rP+AGtr+RG+t+e D+ l++eLl+d+Ke AEH+mL+DLaRND+g
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 285 GASPEILVRQEkrgEDRiVTIRPLAGTRPRGNTPERDAELATELLNDPKEIAEHVMLIDLARNDVG 350
                                                  *********9977534479*********************************************** PP

                                    TIGR00564 319 kvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelide 384
                                                  ++a++gsv v++ + iekyshv+HivS+VeG+lk+++t++D+lra++PaGTlsGAPKvrAmelide
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 351 RIAQIGSVVVTDKMVIEKYSHVQHIVSSVEGKLKPGTTNFDVLRATFPAGTLSGAPKVRAMELIDE 416
                                                  ****************************************************************** PP

                                    TIGR00564 385 lEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakal 450
                                                  lE++kRg+YgGavgylsf g++d ai+iRt v+ +g +yvqA+aG+VaDS+pe+E++Et nKa+a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 417 LEPVKRGLYGGAVGYLSFTGEMDLAITIRTGVIANGNLYVQAAAGVVADSVPESEWQETENKARAV 482
                                                  ****************************************************************** PP

                                    TIGR00564 451 lrai 454
                                                  lra+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 483 LRAA 486
                                                  *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (497 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.95
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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