GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Phyllobacterium endophyticum PEPV15

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_106718131.1 CU100_RS18730 acetolactate synthase 3 large subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_003010935.1:WP_106718131.1
          Length = 601

 Score =  649 bits (1675), Expect = 0.0
 Identities = 324/584 (55%), Positives = 429/584 (73%), Gaps = 5/584 (0%)

Query: 3   SAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHIL 62
           +AE   ++S+SS   EM GAE++V AL ++GV  ++GYPGGAVL IYDEL +Q +  HIL
Sbjct: 2   TAEKLASESHSSQRREMTGAEMVVQALIDQGVTDIFGYPGGAVLPIYDELFQQDRINHIL 61

Query: 63  VRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHA 122
           VRHEQ A HAA+GYAR+TGKVGV LVTSGPG TNAVT +  A +DSIP+V I+G VPT  
Sbjct: 62  VRHEQGAGHAAEGYARSTGKVGVMLVTSGPGATNAVTPLQDALMDSIPLVCISGQVPTSL 121

Query: 123 IGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSR 182
           IG DAFQECDTVGITRP  KHN+LVKDV DLA  + +AF +A TGRPGPV+VD+PKDV  
Sbjct: 122 IGSDAFQECDTVGITRPCTKHNWLVKDVNDLARVLHEAFHVAKTGRPGPVLVDVPKDVQF 181

Query: 183 NACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELR 240
               Y  P+     SY+P  +G    I++AVAL+  A+RP IY+GGGV+ +   AS  LR
Sbjct: 182 ATGIYTPPEVSPRTSYHPRIQGDIEAIKQAVALMLTAKRPVIYSGGGVINSGNEASKLLR 241

Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300
           +L  LT  P+T+TLMGLGA+P + K ++GMLGMHGTYEANM M +CDV++ IGARFDDR+
Sbjct: 242 ELVELTNFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMTMHDCDVMVNIGARFDDRI 301

Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360
            G  + F+  ++K IHIDIDPSSI+K V+VD+P++G+V  VL+++I  I+AS  KP  +A
Sbjct: 302 TGRISGFSPNSKK-IHIDIDPSSINKAVRVDVPVIGDVAHVLEDMIRLIRASSTKPDEKA 360

Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQF 419
           +  WW QI++WRS   L Y R+ ++I PQY +E+++ LTK  D +I ++VGQHQMWAAQF
Sbjct: 361 MGAWWSQIDKWRSRKSLSYTRNKDVIMPQYALERLYALTKDRDTYITTEVGQHQMWAAQF 420

Query: 420 YKFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYD 479
           Y F++P RW+ SGGLGTMG GLP A+G++ A P+  V+ I G+ S+QM +QE+S  +QY+
Sbjct: 421 YHFEKPNRWMTSGGLGTMGYGLPAALGVQIAHPDSLVIDIAGDASVQMNMQEMSAAVQYE 480

Query: 480 TPVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVE 539
            P+KI  LNN Y+GMVRQWQ++ + NR SHSY +ALPDFVKLAEAYG  G+R EK  D++
Sbjct: 481 APIKIFILNNQYMGMVRQWQQLLHGNRLSHSYTEALPDFVKLAEAYGGHGIRCEKPGDLD 540

Query: 540 PALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
            A++E   +K + V  D +     N +PM+ +GK  +EMLL  E
Sbjct: 541 DAIQEMIDVK-KPVLFDCRVANLANCFPMIPSGKAHNEMLLPDE 583


Lambda     K      H
   0.319    0.135    0.407 

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: 936
Number of extensions: 32
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: 585
Length of database: 601
Length adjustment: 37
Effective length of query: 548
Effective length of database: 564
Effective search space:   309072
Effective search space used:   309072
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_106718131.1 CU100_RS18730 (acetolactate synthase 3 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.414534.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-246  804.6   0.1   2.5e-246  804.4   0.1    1.0  1  NCBI__GCF_003010935.1:WP_106718131.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106718131.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.4   0.1  2.5e-246  2.5e-246       1     555 [.      18     580 ..      18     582 .. 0.97

  Alignments for each domain:
  == domain 1  score: 804.4 bits;  conditional E-value: 2.5e-246
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           ++gae++v++l ++gv  +fGyPGGavlpiyd+l+ ++ ++hilvrheq+a haa+Gyar++GkvGv+l+tsG
  NCBI__GCF_003010935.1:WP_106718131.1  18 MTGAEMVVQALIDQGVTDIFGYPGGAVLPIYDELFqQDRINHILVRHEQGAGHAAEGYARSTGKVGVMLVTSG 90 
                                           79*********************************9999********************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vt++ +a +ds+Plv ++Gqv+tsliGsdafqe+d +Git+p+tkh++lvk+++dl+++l+eaf++a
  NCBI__GCF_003010935.1:WP_106718131.1  91 PGATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECDTVGITRPCTKHNWLVKDVNDLARVLHEAFHVA 163
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..ea 216
                                           +tGrPGPvlvd+Pkdv+ a+  ++ +e     +y+p+++g+   ik+a+ l+ +ak+Pv++ GgGvi +  ea
  NCBI__GCF_003010935.1:WP_106718131.1 164 KTGRPGPVLVDVPKDVQFATGIYTPPEVSPRTSYHPRIQGDIEAIKQAVALMLTAKRPVIYSGGGVINSgnEA 236
                                           ********************999999888899***********************************763369 PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+ l+el+e ++ p+t+tl+GlGa+p+  ++ lgmlGmhGt+ean++++++d+++ +Garfddr+tg ++ f+
  NCBI__GCF_003010935.1:WP_106718131.1 237 SKLLRELVELTNFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMTMHDCDVMVNIGARFDDRITGRISGFS 309
                                           9************************************************************************ PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357
                                           p++k ihididP++i+k v+vd+p++Gd+ +vle++++ +++     ++k +  W+++i++w++++ l++ ++
  NCBI__GCF_003010935.1:WP_106718131.1 310 PNSKKIHIDIDPSSINKAVRVDVPVIGDVAHVLEDMIRLIRASstkpDEKAMGaWWSQIDKWRSRKSLSYTRN 382
                                           **************************************9998866553333336******************* PP

                             TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429
                                           ++ i Pq+ +++l+ l+kd ++++tt+vGqhqmwaaqfy+++kp++++tsgGlGtmG+GlPaalG+++a+p++
  NCBI__GCF_003010935.1:WP_106718131.1 383 KDVIMPQYALERLYALTKDrDTYITTEVGQHQMWAAQFYHFEKPNRWMTSGGLGTMGYGLPAALGVQIAHPDS 455
                                           ******************999**************************************************** PP

                             TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                            v++++Gd+s+qmn+qe+s++v+y+ p+ki ilnn+++Gmv+qWq+l++ +r s+++ ++ lpdfvklaeayG
  NCBI__GCF_003010935.1:WP_106718131.1 456 LVIDIAGDASVQMNMQEMSAAVQYEAPIKIFILNNQYMGMVRQWQQLLHGNRLSHSYTEA-LPDFVKLAEAYG 527
                                           ***********************************************************5.************ PP

                             TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                            +gir ekp +l+++++e++ +k+pvl+d +v++ ++++Pm+++G++ +e++ 
  NCBI__GCF_003010935.1:WP_106718131.1 528 GHGIRCEKPGDLDDAIQEMIDVKKPVLFDCRVANLANCFPMIPSGKAHNEMLL 580
                                           **************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (601 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: 26.06
//
[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