GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Herbaspirillum seropedicae SmR1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate HSERO_RS08650 HSERO_RS08650 acetolactate synthase

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



>FitnessBrowser__HerbieS:HSERO_RS08650
          Length = 572

 Score =  874 bits (2258), Expect = 0.0
 Identities = 420/571 (73%), Positives = 491/571 (85%)

Query: 15  AAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAAD 74
           +A ++ GA+ILV  LAEEGVE+V+GYPGGAVLYIYD + KQ KF+HILVRHEQAAVHAAD
Sbjct: 2   SAEQLTGADILVRCLAEEGVEHVFGYPGGAVLYIYDAIFKQDKFQHILVRHEQAAVHAAD 61

Query: 75  GYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTV 134
            Y+R++ KVGVA+VTSGPGVTNAVTG+ATAY+DSIPMVVI+G VP+ AIGQDAFQECDTV
Sbjct: 62  AYSRSSQKVGVAIVTSGPGVTNAVTGLATAYMDSIPMVVISGQVPSTAIGQDAFQECDTV 121

Query: 135 GITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSID 194
           GITRP VKHNFLVKDV+DLA T+KKAF+IA TGRPGPV+VDIPKD++ + C Y YPK+++
Sbjct: 122 GITRPCVKHNFLVKDVKDLAETVKKAFYIATTGRPGPVLVDIPKDITMHTCAYAYPKAVE 181

Query: 195 MRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTL 254
           MRSY PV+KGHSGQIRKA+ LL  AERP IYTGGG++LANA+ EL +L    G+P TNTL
Sbjct: 182 MRSYKPVDKGHSGQIRKALQLLLSAERPMIYTGGGIILANAAPELNKLVDRLGYPCTNTL 241

Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314
           MGLGA+  +S +FVGM GMHGTYEANMAMQ+CDVLIAIGARFDDRVIGNP HF S ARKI
Sbjct: 242 MGLGAYRSSSDKFVGMPGMHGTYEANMAMQHCDVLIAIGARFDDRVIGNPKHFASHARKI 301

Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSV 374
           IHIDIDPSSISKRVKVDIPIVGNVKDVLQEL++Q+ A++ +    AL  WW+QI +WR  
Sbjct: 302 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELLSQLDAAETRQNGAALDAWWKQINEWRKR 361

Query: 375 DCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           DCLK+  S E IKPQ VV+K+WE+TKGDAFI SDVGQHQMWAAQ+Y FD+PRRWINSGGL
Sbjct: 362 DCLKFATSEEFIKPQSVVQKVWEVTKGDAFITSDVGQHQMWAAQYYGFDKPRRWINSGGL 421

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMGVGLPYAMG++ A P+  V  ITGE SIQMCIQEL+TC QY    KI  LNN +LGM
Sbjct: 422 GTMGVGLPYAMGVQMANPDATVACITGEASIQMCIQELATCKQYHLTPKIILLNNRFLGM 481

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQ+I+Y +RYS SYMD+LPDF KLAE+YGHVGM++EK  DV+ ALREAF +KDR VF
Sbjct: 482 VRQWQQIDYGSRYSESYMDSLPDFNKLAESYGHVGMKIEKPGDVDGALREAFAMKDRLVF 541

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           ++F TD TENVWPMV+AGKG++EMLLG+EDL
Sbjct: 542 MNFITDQTENVWPMVKAGKGLTEMLLGSEDL 572


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: 1036
Number of extensions: 31
Number of successful extensions: 1
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: 572
Length adjustment: 36
Effective length of query: 549
Effective length of database: 536
Effective search space:   294264
Effective search space used:   294264
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 HSERO_RS08650 HSERO_RS08650 (acetolactate synthase)
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.16030.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-254  831.2   0.7   2.2e-254  831.0   0.7    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS08650  HSERO_RS08650 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS08650  HSERO_RS08650 acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  831.0   0.7  2.2e-254  2.2e-254       1     554 [.       6     566 ..       6     569 .. 0.98

  Alignments for each domain:
  == domain 1  score: 831.0 bits;  conditional E-value: 2.2e-254
                                  TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvv 67 
                                                l+ga+ilv+ l +egve+vfGyPGGavl iyda++ +++++hilvrheqaa+haad y+r+s kvGv+
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650   6 LTGADILVRCLAEEGVEHVFGYPGGAVLYIYDAIFkQDKFQHILVRHEQAAVHAADAYSRSSQKVGVA 73 
                                                68*********************************999****************************** PP

                                  TIGR00118  68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135
                                                ++tsGPG tn+vtg+atay+ds+P+vv++Gqv++++iG+dafqe+d +Git+p++kh+flvk+++dl+
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650  74 IVTSGPGVTNAVTGLATAYMDSIPMVVISGQVPSTAIGQDAFQECDTVGITRPCVKHNFLVKDVKDLA 141
                                                ******************************************************************** PP

                                  TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkP 203
                                                e++k+af+ia+tGrPGPvlvd+Pkd+t +++ + +++ ve+++ykp  kgh  qi+kal+l+ +a++P
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 142 ETVKKAFYIATTGRPGPVLVDIPKDITMHTCAYAYPKAVEMRSYKPVDKGHSGQIRKALQLLLSAERP 209
                                                ******************************************************************** PP

                                  TIGR00118 204 vllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                                +++ GgG+i a+a  el++l++rl  p t tl+GlGa+ +   +++gm GmhGt+ean+a++++d+li
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 210 MIYTGGGIILANAAPELNKLVDRLGYPCTNTLMGLGAYRSSSDKFVGMPGMHGTYEANMAMQHCDVLI 277
                                                ******************************************************************** PP

                                  TIGR00118 272 avGarfddrvtgnlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklkee....ek 334
                                                a+Garfddrv gn ++fa++a+ iihididP++i+k vkvdipivG++k vl+ell++l +     + 
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 278 AIGARFDDRVIGNPKHFASHARkIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELLSQLDAAetrqNG 345
                                                ********************965***********************************9988443222 PP

                                  TIGR00118 335 keke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkpr 401
                                                   + W+++i+ew+k+ +lk+ ++ee ikPq+v++++++++k++a++t+dvGqhqmwaaq+y ++kpr
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 346 AALDaWWKQINEWRKRDCLKFATSEEFIKPQSVVQKVWEVTKGDAFITSDVGQHQMWAAQYYGFDKPR 413
                                                23346*************************************************************** PP

                                  TIGR00118 402 kfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGm 469
                                                ++i+sgGlGtmG GlP a+G+++a+p++tv ++tG++s+qm +qel+t+++y++  ki++lnn++lGm
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 414 RWINSGGLGTMGVGLPYAMGVQMANPDATVACITGEASIQMCIQELATCKQYHLTPKIILLNNRFLGM 481
                                                ******************************************************************** PP

                                  TIGR00118 470 vkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdk 536
                                                v+qWq++ y  ryse+++ s lpdf+klae+yG++g++iekp +++ +l+ea+++k ++v++++  d+
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 482 VRQWQQIDYGSRYSESYMDS-LPDFNKLAESYGHVGMKIEKPGDVDGALREAFAMKdRLVFMNFITDQ 548
                                                *******************5.*******************************9988799********* PP

                                  TIGR00118 537 eeevlPmvapGagldelv 554
                                                +e+v+Pmv  G+gl+e++
  lcl|FitnessBrowser__HerbieS:HSERO_RS08650 549 TENVWPMVKAGKGLTEML 566
                                                ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 11.43
//
[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