Alignments for a candidate for ilvI in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhodobacter sphaeroides ATCC 17029

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011840925.1 RSPH17029_RS06560 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000015985.1:WP_011840925.1
          Length = 588

 Score =  597 bits (1538), Expect = e-175
 Identities = 300/566 (53%), Positives = 400/566 (70%), Gaps = 5/566 (0%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78
           M GA ++V AL ++GV+ V+GYPGGAVL IYDE+ +Q    HILVRHEQ AVH A+GYAR
Sbjct: 9   MSGARMVVQALKDQGVDTVFGYPGGAVLPIYDEIFQQNDIRHILVRHEQGAVHMAEGYAR 68

Query: 79  ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138
           +TGK GV LVTSGPG TNAVTG+  A +DSIP+VV++G VPT  IG D FQE DTVGITR
Sbjct: 69  STGKPGVVLVTSGPGATNAVTGLVDALMDSIPLVVLSGQVPTFMIGTDGFQEADTVGITR 128

Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198
           P  KHN+LVKD   LA TI +AF +A  GRPGPV+VDIPKDV      Y+ P+   +  Y
Sbjct: 129 PCTKHNWLVKDTARLAETIHQAFHVATHGRPGPVLVDIPKDVQFATATYQPPQKARVDHY 188

Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLMG 256
            P  KG    I + V L++ AERP  YTGGGV+ +   A+  LR+    TG P+T+TLMG
Sbjct: 189 QPKVKGDIETITRMVELIETAERPVFYTGGGVINSGSAANQLLREFVDATGFPITSTLMG 248

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGA+P + K ++GMLGMHG YEAN+AM  CD++I +GARFDDR+ G    F+  ++K +H
Sbjct: 249 LGAYPASGKGWLGMLGMHGLYEANLAMHGCDLMINVGARFDDRITGRVKDFSPFSQK-VH 307

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           IDIDPSSI+K ++ D+PI+G+V  VL++ +   K+   K  REALA WW+QI +W++V+C
Sbjct: 308 IDIDPSSINKVIRADVPIIGDVGHVLEDALRLWKSRGRKVNREALADWWKQIAEWKAVNC 367

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           L Y  SS++IKPQ+ ++++  LTKG D +I ++VGQHQMWAAQF  F+ P RW+ SGGLG
Sbjct: 368 LDYTPSSKLIKPQHALQRLEALTKGMDRYITTEVGQHQMWAAQFLGFEGPNRWMTSGGLG 427

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP ++G++ A PE  V+ I G+ S  M +QE+ T +Q+  PVK   LNN  LGMV
Sbjct: 428 TMGYGLPASIGVQVAHPEALVINIAGDASFLMNMQEIGTAMQFRLPVKQFILNNERLGMV 487

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQ++ +  RYS S+ ++LPDFVKLAEA+G  G++    +D++ A+RE     D  V  
Sbjct: 488 RQWQQLLHGQRYSQSWSESLPDFVKLAEAFGAKGIQCADPADLDDAIREMIAY-DGPVVF 546

Query: 556 DFQTDPTENVWPMVQAGKGISEMLLG 581
           D   +  EN +PM+ +G+  +EMLLG
Sbjct: 547 DCLVEKHENCFPMIPSGRPHNEMLLG 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: 936
Number of extensions: 35
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: 588
Length adjustment: 37
Effective length of query: 548
Effective length of database: 551
Effective search space:   301948
Effective search space used:   301948
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_011840925.1 RSPH17029_RS06560 (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.2041.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-238  776.2   0.0   9.8e-238  776.0   0.0    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011840925.1  RSPH17029_RS06560 acetolactate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011840925.1  RSPH17029_RS06560 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  776.0   0.0  9.8e-238  9.8e-238       1     554 [.       9     570 ..       9     573 .. 0.97

  Alignments for each domain:
  == domain 1  score: 776.0 bits;  conditional E-value: 9.8e-238
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++hilvrheq+a+h+a+Gyar++Gk+Gvvl
  lcl|NCBI__GCF_000015985.1:WP_011840925.1   9 MSGARMVVQALKDQGVDTVFGYPGGAVLPIYDEIFqQNDIRHILVRHEQGAVHMAEGYARSTGKPGVVL 77 
                                               79*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+++a +ds+Plvvl+Gqv+t +iG+d fqe+d +Git+p+tkh++lvk+++ l+e+
  lcl|NCBI__GCF_000015985.1:WP_011840925.1  78 VTSGPGATNAVTGLVDALMDSIPLVVLSGQVPTFMIGTDGFQEADTVGITRPCTKHNWLVKDTARLAET 146
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +++af++a+ GrPGPvlvd+Pkdv+ a+ +++ ++k  +  y+p+vkg+   i + +elie+a++Pv +
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 147 IHQAFHVATHGRPGPVLVDIPKDVQFATATYQPPQKARVDHYQPKVKGDIETITRMVELIETAERPVFY 215
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                                GgGvi ++  a++ l+e+++++  p+t+tl+GlGa+p+  +  lgmlGmhG +eanla++ +dl+i v
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 216 TGGGVINSGsaANQLLREFVDATGFPITSTLMGLGAYPASGKGWLGMLGMHGLYEANLAMHGCDLMINV 284
                                               ******76422678899**************************************************** PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddr+tg ++ f+p ++ +hididP++i+k++++d+pi+Gd+ +vle+ l+  k++    +++   
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 285 GARFDDRITGRVKDFSPFSQKVHIDIDPSSINKVIRADVPIIGDVGHVLEDALRLWKSRgrkvNREALA 353
                                               ***************************************************998877766655555555 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                                W+++i+ewk+ ++l +  +++ ikPq+ +++l  l+k+ + ++tt+vGqhqmwaaqf+ ++ p++++t
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 354 dWWKQIAEWKAVNCLDYTPSSKLIKPQHALQRLEALTKGmDRYITTEVGQHQMWAAQFLGFEGPNRWMT 422
                                               6*************************************999**************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG+GlPa++G++va+pe+ v++++Gd+sf mn+qe+ t++++ +pvk  ilnne lGmv+qWq
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 423 SGGLGTMGYGLPASIGVQVAHPEALVINIAGDASFLMNMQEIGTAMQFRLPVKQFILNNERLGMVRQWQ 491
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543
                                               +l++ +rys++  +s lpdfvklaea+G+kgi+ ++p++l+++++e+++ ++pv++d  v+k+e+++Pm
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 492 QLLHGQRYSQSWSES-LPDFVKLAEAFGAKGIQCADPADLDDAIREMIAYDGPVVFDCLVEKHENCFPM 559
                                               ***********9995.***************************************************** PP

                                 TIGR00118 544 vapGagldelv 554
                                               +++G   +e++
  lcl|NCBI__GCF_000015985.1:WP_011840925.1 560 IPSGRPHNEML 570
                                               *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (588 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: 11.28
//
[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