Alignments for a candidate for ilvI in Herbaspirillum seropedicae SmR1

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.16195.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: 12.59
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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