GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Thermophagus xiamenensis HS1

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_044138357.1 GQW_RS0101510 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000220155.1:WP_044138357.1
          Length = 569

 Score =  486 bits (1251), Expect = e-141
 Identities = 269/577 (46%), Positives = 351/577 (60%), Gaps = 15/577 (2%)

Query: 29  RPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFD-SKKLRHVLVRHEQG 87
           + K     +++G++AVI+SL   G  +IFG PGGA++P+YD L D  K+L HVL RHEQG
Sbjct: 2   KEKTTKTTRMSGSEAVIQSLLREGTSIIFGYPGGAIMPIYDALHDHQKELHHVLTRHEQG 61

Query: 88  AGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAF 147
           A HAA GYA VTG+VGVC ATSGPGATN VT LA+A MDS PVV ITGQV   L+GTDAF
Sbjct: 62  ALHAAEGYAKVTGKVGVCFATSGPGATNTVTGLANAMMDSTPVVLITGQVVSSLLGTDAF 121

Query: 148 QEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFS 207
           QE D+ G+T P+TK N+ VR  +DIP  +A AF+IA SGRPG V++DI KD    Q  F 
Sbjct: 122 QETDVVGVTQPVTKWNYQVRRAEDIPAAIARAFYIARSGRPGPVVIDITKDAQINQLDFY 181

Query: 208 WPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGI 267
           + P   +  Y P       Q+ EAA+LI  ++KP+  VG GVI G A ++L +  E +GI
Sbjct: 182 YEPVKSIRSYTPEYPADLAQIEEAARLINLSKKPLALVGQGVIIGNAEKELLDFLEKSGI 241

Query: 268 PVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFA 327
           P   TL+   A P  H  N+GM GMHG          +DL++A+G RFDDRVTG L  +A
Sbjct: 242 PAAWTLLGLSAVPSDHPLNVGMLGMHGNYGPNIKTNEADLIVAIGMRFDDRVTGDLSRYA 301

Query: 328 PEAKVIHADIDPAEIGKNRHADVPIVGDVK---AVITELIAMLRHHHIPGTIEMADWWAY 384
             AK+IH +IDPAEI KN HADVPI+G+VK    ++TE I    H       E      Y
Sbjct: 302 TNAKIIHMEIDPAEINKNVHADVPILGNVKKTLPLLTEKIVKNDHSDWLKEFEACQRVEY 361

Query: 385 LNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPR 444
              + K       P   G    E V+ K+ +    DA+ V  VGQHQM  A++ ++++ R
Sbjct: 362 NRIIEK----QLNPIEKGITMGE-VVAKVSQAFDNDAIMVTDVGQHQMMGARYFKFKQSR 416

Query: 445 SWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVAL 504
           S + SGGLGTMGF +PAAMGAK+  P  +V    GDG  QMT QEL T     IPVK+ L
Sbjct: 417 SVVTSGGLGTMGFGLPAAMGAKLGAPDRQVCVFVGDGGLQMTIQELGTIYQTQIPVKIVL 476

Query: 505 INNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVI 564
           +NN  LGMVRQWQ LF+ +RY+ T+L       PDF  +A+      L+    +D+ + I
Sbjct: 477 LNNNFLGMVRQWQELFFDKRYASTELIN-----PDFQTIAKGYHIPSLKVSERQDLDEAI 531

Query: 565 NQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEIQ 601
            Q     D P +++ IV  +  V+PMV AG S  +I+
Sbjct: 532 -QKMVEADGPFLLEVIVEKEGNVFPMVPAGASVSDIR 567


Lambda     K      H
   0.319    0.136    0.414 

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: 916
Number of extensions: 39
Number of successful extensions: 3
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: 618
Length of database: 569
Length adjustment: 37
Effective length of query: 581
Effective length of database: 532
Effective search space:   309092
Effective search space used:   309092
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: 53 (25.0 bits)

Align candidate WP_044138357.1 GQW_RS0101510 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.3397911.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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-222  725.5   1.8   2.2e-222  725.4   1.8    1.0  1  NCBI__GCF_000220155.1:WP_044138357.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_044138357.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.4   1.8  2.2e-222  2.2e-222       1     553 [.      11     566 ..      11     569 .] 0.97

  Alignments for each domain:
  == domain 1  score: 725.4 bits;  conditional E-value: 2.2e-222
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                           ++g+e++++sl +eg  ++fGyPGGa++piydal+  ++el+h+l+rheq+a haa+Gya+++GkvGv++ats
  NCBI__GCF_000220155.1:WP_044138357.1  11 MSGSEAVIQSLLREGTSIIFGYPGGAIMPIYDALHdhQKELHHVLTRHEQGALHAAEGYAKVTGKVGVCFATS 83 
                                           79*********************************88899********************************* PP

                             TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafei 144
                                           GPGatn+vtg+a+a++ds+P+v++tGqv +sl+G+dafqe d++G+t+pvtk++++v++aed+p+ + +af+i
  NCBI__GCF_000220155.1:WP_044138357.1  84 GPGATNTVTGLANAMMDSTPVVLITGQVVSSLLGTDAFQETDVVGVTQPVTKWNYQVRRAEDIPAAIARAFYI 156
                                           ************************************************************************* PP

                             TIGR00118 145 astGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeas 217
                                           a +GrPGPv++d+ kd + +++++ +e   ++++y p+  ++ +qi++a+ li+ +kkP+ lvG Gvii++a+
  NCBI__GCF_000220155.1:WP_044138357.1 157 ARSGRPGPVVIDITKDAQINQLDFYYEPVKSIRSYTPEYPADLAQIEEAARLINLSKKPLALVGQGVIIGNAE 229
                                           ***************************999******************************************* PP

                             TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap 290
                                           +el ++ e+  ip + tllGl a+p+dhpl +gmlGmhG +  n+  +eadl++a+G+rfddrvtg+l+++a+
  NCBI__GCF_000220155.1:WP_044138357.1 230 KELLDFLEKSGIPAAWTLLGLSAVPSDHPLNVGMLGMHGNYGPNIKTNEADLIVAIGMRFDDRVTGDLSRYAT 302
                                           ************************************************************************* PP

                             TIGR00118 291 eakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilk.....ldeee 358
                                           +akiih++idPaei+knv++d+pi G++kk l  l +k+ ++++++  Wl++ e  ++    +     l+  e
  NCBI__GCF_000220155.1:WP_044138357.1 303 NAKIIHMEIDPAEINKNVHADVPILGNVKKTLPLLTEKIVKNDHSD--WLKEFEACQRVEYNRiiekqLNPIE 373
                                           ****************************************999988..9999887654333221001255667 PP

                             TIGR00118 359 esikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431
                                           + i   +v+ ++s+  +++ai+ tdvGqhqm  a+++k+k++r+ +tsgGlGtmGfGlPaa+Gak++ p+ +v
  NCBI__GCF_000220155.1:WP_044138357.1 374 KGITMGEVVAKVSQAFDNDAIMVTDVGQHQMMGARYFKFKQSRSVVTSGGLGTMGFGLPAAMGAKLGAPDRQV 446
                                           889999******************************************************************* PP

                             TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504
                                              +Gdg++qm++qel ti + +ipvkiv+lnn++lGmv+qWqelf+++ry++t+l +  pdf+ +a++y + 
  NCBI__GCF_000220155.1:WP_044138357.1 447 CVFVGDGGLQMTIQELGTIYQTQIPVKIVLLNNNFLGMVRQWQELFFDKRYASTELIN--PDFQTIAKGYHIP 517
                                           *********************************************************7..************* PP

                             TIGR00118 505 giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                           +++++++++l+e++++++e ++p ll+v v+ke +v+Pmv+ Ga+++++
  NCBI__GCF_000220155.1:WP_044138357.1 518 SLKVSERQDLDEAIQKMVEADGPFLLEVIVEKEGNVFPMVPAGASVSDI 566
                                           ********************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (569 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: 27.52
//
[ok]

This GapMind analysis is from Jul 26 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:

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