Alignments for a candidate for ilvI in Rhodopseudomonas palustris CGA009

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhodopseudomonas palustris CGA009

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011157586.1 TX73_RS10350 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000195775.1:WP_011157586.1
          Length = 592

 Score =  652 bits (1683), Expect = 0.0
 Identities = 319/579 (55%), Positives = 430/579 (74%), Gaps = 9/579 (1%)

Query: 9   ADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQA 68
           +DSNS    +M GA ++V A+ + GVE+++GYPGGAVL IYDE+ +Q+  +HILVRHEQ 
Sbjct: 2   SDSNSHDPNQMTGAAMIVRAMKDHGVEHIFGYPGGAVLPIYDEIFQQSDVQHILVRHEQG 61

Query: 69  AVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAF 128
           A HAA+GYAR+TGK GV LVTSGPG TN VT +A A +DSIP+V ITG VPTH IG DAF
Sbjct: 62  AGHAAEGYARSTGKPGVVLVTSGPGATNMVTPLADALMDSIPLVCITGQVPTHLIGNDAF 121

Query: 129 QECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYE 188
           QECDTVGITRP  KHN+LV+ + DLA  + +AF++A +GRPGPVVVD+PKDV      Y 
Sbjct: 122 QECDTVGITRPCTKHNWLVRRIEDLAKVLHEAFYVATSGRPGPVVVDVPKDVQFATGTYH 181

Query: 189 YPKSIDMR-SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAAL 245
            P+  D+  SY P  KG   QIRKAVALL  A+RP IY+GGGV+ +   AS  LR+L  +
Sbjct: 182 PPRKADVHVSYVPNKKGDPAQIRKAVALLANAKRPVIYSGGGVINSGPEASRLLRELVEI 241

Query: 246 TGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPA 305
           T  P+T+TLMGLGA+P + K ++GMLGMHGTYEANM M +CDV++ IGARFDDR+ G   
Sbjct: 242 TDFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMTMHDCDVMLCIGARFDDRITGRTD 301

Query: 306 HFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWW 365
            F   A+K IHIDIDPSSI+K ++VD+PI+G+V  VL +L++  KA   KP    +  WW
Sbjct: 302 AFAPNAKK-IHIDIDPSSINKNIRVDVPIIGDVATVLADLLSAFKAEAKKPD---IKPWW 357

Query: 366 EQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDE 424
           +Q+  WR+ + L Y +++++I PQY +++++E T+G D +I ++VGQHQMWAAQFY F++
Sbjct: 358 QQVATWRARNSLAYKKNNDVIMPQYAIQRLYEATRGRDTYITTEVGQHQMWAAQFYGFEQ 417

Query: 425 PRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKI 484
           P+RW+ SGGLGTMG GLP A+G++ A  +  V+ I G+ S+QM IQE++T +QY+ P+KI
Sbjct: 418 PKRWMTSGGLGTMGYGLPAALGVQVAHRDSLVIDIAGDASVQMTIQEMATAVQYELPIKI 477

Query: 485 CSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALRE 544
             LNN Y+GMVRQWQ++ + NR SHSY +A+PDFVKLAEAYG VGM+V K SD++ A+++
Sbjct: 478 FILNNQYMGMVRQWQQLLHGNRLSHSYTEAMPDFVKLAEAYGAVGMQVVKPSDLDGAIQD 537

Query: 545 AFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
             ++ ++ V  D +    EN +PM+ +GK  +EMLL AE
Sbjct: 538 MIKV-NKPVLFDCRVAALENCFPMIPSGKAHNEMLLPAE 575


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: 958
Number of extensions: 35
Number of successful extensions: 8
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: 592
Length adjustment: 37
Effective length of query: 548
Effective length of database: 555
Effective search space:   304140
Effective search space used:   304140
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_011157586.1 TX73_RS10350 (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.5881.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-252  823.7   0.7     4e-252  823.5   0.7    1.0  1  lcl|NCBI__GCF_000195775.1:WP_011157586.1  TX73_RS10350 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011157586.1  TX73_RS10350 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  823.5   0.7    4e-252    4e-252       1     554 [.      12     571 ..      12     574 .. 0.98

  Alignments for each domain:
  == domain 1  score: 823.5 bits;  conditional E-value: 4e-252
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga ++v+++k++gve++fGyPGGavlpiyd+++ +s+++hilvrheq+a haa+Gyar++Gk+Gvvl
  lcl|NCBI__GCF_000195775.1:WP_011157586.1  12 MTGAAMIVRAMKDHGVEHIFGYPGGAVLPIYDEIFqQSDVQHILVRHEQGAGHAAEGYARSTGKPGVVL 80 
                                               79*********************************99******************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vt++a+a +ds+Plv +tGqv+t+liG+dafqe+d +Git+p+tkh++lv++ edl+++
  lcl|NCBI__GCF_000195775.1:WP_011157586.1  81 VTSGPGATNMVTPLADALMDSIPLVCITGQVPTHLIGNDAFQECDTVGITRPCTKHNWLVRRIEDLAKV 149
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelp.gykptvkghklqikkaleliekakkPvl 205
                                               l+eaf++a++GrPGPv+vd+Pkdv+ a+ +++ ++k ++  +y p++kg+++qi+ka+ l+++ak+Pv+
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 150 LHEAFYVATSGRPGPVVVDVPKDVQFATGTYHPPRKADVHvSYVPNKKGDPAQIRKAVALLANAKRPVI 218
                                               *******************************99988777549*************************** PP

                                 TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               + GgGvi +  eas+ l+el+e ++ p+t+tl+GlGa+p+  ++ lgmlGmhGt+ean++++++d++++
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 219 YSGGGVINSgpEASRLLRELVEITDFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMTMHDCDVMLC 287
                                               *******8744699******************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.ekkeke.W 339
                                               +Garfddr+tg  + fap+ak ihididP++i+kn++vd+pi+Gd+ +vl++ll++ k+e +k +++ W
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 288 IGARFDDRITGRTDAFAPNAKKIHIDIDPSSINKNIRVDVPIIGDVATVLADLLSAFKAEaKKPDIKpW 356
                                               ********************************************************999867778889* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               +++++ w++++ l+++++++ i Pq+ i++l++ +++ ++++tt+vGqhqmwaaqfy +++p++++tsg
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 357 WQQVATWRARNSLAYKKNNDVIMPQYAIQRLYEATRGrDTYITTEVGQHQMWAAQFYGFEQPKRWMTSG 425
                                               ***********************************9989****************************** PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG+GlPaalG++va+ ++ v++++Gd+s+qm++qe++t+v+y++p+ki ilnn+++Gmv+qWq+l
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 426 GLGTMGYGLPAALGVQVAHRDSLVIDIAGDASVQMTIQEMATAVQYELPIKIFILNNQYMGMVRQWQQL 494
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmva 545
                                               ++ +r s+++ ++ +pdfvklaeayG++g+++ kp++l+ ++++++++++pvl+d +v+  e+++Pm++
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 495 LHGNRLSHSYTEA-MPDFVKLAEAYGAVGMQVVKPSDLDGAIQDMIKVNKPVLFDCRVAALENCFPMIP 562
                                               ************5.******************************************************* PP

                                 TIGR00118 546 pGagldelv 554
                                               +G++ +e++
  lcl|NCBI__GCF_000195775.1:WP_011157586.1 563 SGKAHNEML 571
                                               *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (592 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: 11.00
//
[ok]

This GapMind analysis is from Apr 10 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:

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