Alignments for a candidate for ilvI in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Saccharomonospora cyanea NA-134

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_043536172.1 SACCYDRAFT_RS05075 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000244975.1:WP_043536172.1
          Length = 620

 Score =  900 bits (2327), Expect = 0.0
 Identities = 438/615 (71%), Positives = 507/615 (82%), Gaps = 3/615 (0%)

Query: 1   MSAPTKPHSPTFKPEPHSA--ANEPKHPAARPKHVALQQLTGAQAVIRSLEELGVDVIFG 58
           M++ T     T    P+SA  AN    P   P      ++TGAQ+++RSLE +GV+V+FG
Sbjct: 1   MTSATSRSDATAGSTPNSASPANSGPRPKPTPPAGVPVRVTGAQSLVRSLEAVGVEVVFG 60

Query: 59  IPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVT 118
           IPGG +LP YDPL DS K+RHVLVRHEQGAGHAA+GYA  TGRVGVCMATSGPGATNLVT
Sbjct: 61  IPGGTILPAYDPLLDSTKVRHVLVRHEQGAGHAATGYAQATGRVGVCMATSGPGATNLVT 120

Query: 119 PLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAE 178
           PLADA MDS+PVVAITGQ  R LIG+DAFQEADI GITMPITKHNFLV    DIPRV+AE
Sbjct: 121 PLADAYMDSVPVVAITGQQTRALIGSDAFQEADICGITMPITKHNFLVTEPADIPRVIAE 180

Query: 179 AFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQVREAAKLIAAA 238
           AFH+A++GRPG VLVDIPKDVLQ   +F+WPP + LPGY+P  +PH +QVREAA+LI  A
Sbjct: 181 AFHLASTGRPGPVLVDIPKDVLQETTSFAWPPELNLPGYRPTLRPHGKQVREAARLITQA 240

Query: 239 RKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAA 298
           R+PV YVGGGV++  A EQLREL ELTGIPVVTTLMARG FPDSHRQ+LGMPGMHG+VAA
Sbjct: 241 RRPVFYVGGGVLKAGAAEQLRELVELTGIPVVTTLMARGVFPDSHRQHLGMPGMHGSVAA 300

Query: 299 VAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKA 358
           VAA+QR+DLL+ALG RFDDRVTG+L+SFAPEAKV+HADIDPAEI KNR ADVPIVGD   
Sbjct: 301 VAAMQRADLLVALGARFDDRVTGRLESFAPEAKVVHADIDPAEISKNRKADVPIVGDCAE 360

Query: 359 VITELIAMLRHHHIPG-TIEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIA 417
           +ITELI  +R+    G + ++A WW  LN  R T+P  Y   SDG+L+P+YVIE++G++ 
Sbjct: 361 IITELIDAVRNETSYGESADLAAWWLQLNSWRDTFPAGYEWPSDGTLAPQYVIERIGKLV 420

Query: 418 GPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAI 477
           GPDA++ AGVGQHQMWAAQFI YE+PR+W+NSGGLGTMGFA+PAAMGA+   P  +VWAI
Sbjct: 421 GPDAIYAAGVGQHQMWAAQFISYEQPRTWINSGGLGTMGFAVPAAMGAQFGRPDKQVWAI 480

Query: 478 DGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRI 537
           DGDGCFQMTNQELATCA+EG P+KVA+INNGNLGMVRQWQ+LFYAERYS TDL TH HRI
Sbjct: 481 DGDGCFQMTNQELATCAIEGAPIKVAVINNGNLGMVRQWQNLFYAERYSNTDLGTHKHRI 540

Query: 538 PDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSN 597
           PDF  LAEALGC GLRCE ++ V D I +A  IND PVVIDF+VG DAQVWPMVAAGTSN
Sbjct: 541 PDFALLAEALGCAGLRCETKDSVDDTIRRAMEINDRPVVIDFVVGKDAQVWPMVAAGTSN 600

Query: 598 DEIQAARGIRPLFDD 612
           DEI AARGIRPLFD+
Sbjct: 601 DEIMAARGIRPLFDE 615


Lambda     K      H
   0.319    0.136    0.414 

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: 1287
Number of extensions: 45
Number of successful extensions: 2
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: 618
Length of database: 620
Length adjustment: 37
Effective length of query: 581
Effective length of database: 583
Effective search space:   338723
Effective search space used:   338723
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_043536172.1 SACCYDRAFT_RS05075 (acetolactate synthase 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.24510.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-234  764.7   0.0   2.9e-234  764.6   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_043536172.1  SACCYDRAFT_RS05075 acetolactate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_043536172.1  SACCYDRAFT_RS05075 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  764.6   0.0  2.9e-234  2.9e-234       2     555 ..      41     605 ..      40     607 .. 0.97

  Alignments for each domain:
  == domain 1  score: 764.6 bits;  conditional E-value: 2.9e-234
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+ lv+sl++ gve+vfG+PGG++lp yd l  + +++h+lvrheq+a haa Gya+a+G+vGv++a
  lcl|NCBI__GCF_000244975.1:WP_043536172.1  41 TGAQSLVRSLEAVGVEVVFGIPGGTILPAYDPLLdSTKVRHVLVRHEQGAGHAATGYAQATGRVGVCMA 109
                                               79******************************997889******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvt++a+ay+dsvP+v++tGq +++liGsdafqe+di Git+p+tkh+flv++++d+p+++
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 110 TSGPGATNLVTPLADAYMDSVPVVAITGQQTRALIGSDAFQEADICGITMPITKHNFLVTEPADIPRVI 178
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                eaf++astGrPGPvlvd+Pkdv ++++++  + +++lpgy+pt+++h +q+++a+ li++a++Pv +v
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 179 AEAFHLASTGRPGPVLVDIPKDVLQETTSFAWPPELNLPGYRPTLRPHGKQVREAARLITQARRPVFYV 247
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv++a+a e+l+el+e + ipv+ttl+  G fp+ h++ lgm GmhG+ +a  a++ adll+a+Gar
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 248 GGGVLKAGAAEQLRELVELTGIPVVTTLMARGVFPDSHRQHLGMPGMHGSVAAVAAMQRADLLVALGAR 316
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wl 340
                                               fddrvtg l++fapeak++h didPaei+kn+k+d+pivGd+ ++++el++++++e    e+ +   W+
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 317 FDDRVTGRLESFAPEAKVVHADIDPAEISKNRKADVPIVGDCAEIITELIDAVRNEtsygESADLAaWW 385
                                               *****************************************************99988887777778** PP

                                 TIGR00118 341 ekieewkkeyilkldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                                ++++w+++ +  ++  ++  ++Pq+vi+++ kl+  +ai++++vGqhqmwaaqf ++++pr++i+sgG
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 386 LQLNSWRDTFPAGYEWPSDGtLAPQYVIERIGKLVGPDAIYAAGVGQHQMWAAQFISYEQPRTWINSGG 454
                                               ***********9999766544************************************************ PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmGf +Paa+Ga+ + p+++v a++Gdg fqm+ qel+t++  + p+k+ ++nn  lGmv+qWq+lf
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 455 LGTMGFAVPAAMGAQFGRPDKQVWAIDGDGCFQMTNQELATCAIEGAPIKVAVINNGNLGMVRQWQNLF 523
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklas...elpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlP 542
                                               y erys+t l++     pdf+ laea+G  g+r e+++ +++ +++a+e + +pv++d++v k+++v+P
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 524 YAERYSNTDLGThkhRIPDFALLAEALGCAGLRCETKDSVDDTIRRAMEINdRPVVIDFVVGKDAQVWP 592
                                               ********987522257********************************9879**************** PP

                                 TIGR00118 543 mvapGagldelve 555
                                               mva G+++de++ 
  lcl|NCBI__GCF_000244975.1:WP_043536172.1 593 MVAAGTSNDEIMA 605
                                               **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (620 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.01
//
[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