Alignments for a candidate for ilvI in Frankia alni ACN14A

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Frankia alni ACN14A

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_083866922.1 FRAAL_RS25490 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000058485.1:WP_083866922.1
          Length = 621

 Score =  848 bits (2192), Expect = 0.0
 Identities = 415/614 (67%), Positives = 494/614 (80%), Gaps = 16/614 (2%)

Query: 9   SPTFKPEPHSAANEPKHPAARPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVY 68
           +P F+P P   A     P      +  +++TGAQ+++ SLE +G DV+FGIPGGA+LP Y
Sbjct: 4   APAFRP-PRPPAVADSRPVKEDAQMT-REITGAQSLVHSLEAVGADVVFGIPGGAILPAY 61

Query: 69  DPLFDSKKLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSI 128
           DPLFDS ++RH+LVRHEQGAGHAA GYA  TGRVGVCMATSGPGATNLVTP+ADA MDS+
Sbjct: 62  DPLFDSTRVRHILVRHEQGAGHAAEGYAQATGRVGVCMATSGPGATNLVTPIADAYMDSV 121

Query: 129 PVVAITGQVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRP 188
           P+VAITGQV    IGTDAFQEADI GIT+PITKHNFLV+S DDIPR +AEAFH+A +GRP
Sbjct: 122 PMVAITGQVASAAIGTDAFQEADICGITLPITKHNFLVQSVDDIPRTIAEAFHLAGTGRP 181

Query: 189 GAVLVDIPKDVLQGQCTF----SWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLY 244
           G VLVD+PKD+LQ   +      WPP ++LPGY+P T+PH++QVREAAKLI+A+R+PVLY
Sbjct: 182 GPVLVDLPKDILQSVTSVLPHEIWPPTLDLPGYRPITRPHNKQVREAAKLISASRRPVLY 241

Query: 245 VGGGVIRGEATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQR 304
           +GGGV++  A  +LR LAE+TGIPVVTTLMARGAFPDSH Q+LGMPGMHG+VAAV ALQ+
Sbjct: 242 IGGGVLKARAAAELRTLAEMTGIPVVTTLMARGAFPDSHPQHLGMPGMHGSVAAVTALQK 301

Query: 305 SDLLIALGTRFDDRVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELI 364
           +DLLI LG RFDDRVTG+L SFAP+A +IHADIDPAEIGKNR ADVPIVGD + VI ELI
Sbjct: 302 ADLLITLGARFDDRVTGRLASFAPKAAIIHADIDPAEIGKNRTADVPIVGDCREVINELI 361

Query: 365 AMLRHHHIPGTIEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFV 424
           A L     P   E+  WW  L+G R+TYPL Y   +DGSL+P++VIE+LG I+GP+ +F 
Sbjct: 362 AALAAEPRP---ELDAWWHTLDGWRRTYPLGYDTPADGSLAPQHVIERLGRISGPETIFA 418

Query: 425 AGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQ 484
           AGVGQHQMWAAQFI YE P +WLNSGG GTMGFA+PAAMGAK+  P T VWAIDGDGCFQ
Sbjct: 419 AGVGQHQMWAAQFISYEHPYTWLNSGGAGTMGFAVPAAMGAKVGRPDTTVWAIDGDGCFQ 478

Query: 485 MTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHS-------HRI 537
           MTNQELATCA+EGIP+KVA+INNG+LGMVRQWQ+LFY +RYS T+L TH         R+
Sbjct: 479 MTNQELATCALEGIPIKVAVINNGSLGMVRQWQTLFYDKRYSNTELGTHPGSPRTGVKRV 538

Query: 538 PDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSN 597
           PDFV+LAEALGCVGLRC+   +V   I +A AI+D PVV+DF+V  DA VWPMVAAG SN
Sbjct: 539 PDFVRLAEALGCVGLRCDSAAEVDATIEKAMAIDDAPVVVDFVVHPDAMVWPMVAAGASN 598

Query: 598 DEIQAARGIRPLFD 611
           DEI+ AR + P FD
Sbjct: 599 DEIRVARDLAPDFD 612


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: 1294
Number of extensions: 45
Number of successful extensions: 4
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: 621
Length adjustment: 37
Effective length of query: 581
Effective length of database: 584
Effective search space:   339304
Effective search space used:   339304
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_083866922.1 FRAAL_RS25490 (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.2124.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.4e-232  756.3   0.0   1.1e-231  756.0   0.0    1.0  1  lcl|NCBI__GCF_000058485.1:WP_083866922.1  FRAAL_RS25490 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_083866922.1  FRAAL_RS25490 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  756.0   0.0  1.1e-231  1.1e-231       2     553 ..      32     601 ..      31     605 .. 0.96

  Alignments for each domain:
  == domain 1  score: 756.0 bits;  conditional E-value: 1.1e-231
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+ lv+sl++ g ++vfG+PGGa+lp yd l+ +  ++hilvrheq+a haa+Gya+a+G+vGv++a
  lcl|NCBI__GCF_000058485.1:WP_083866922.1  32 TGAQSLVHSLEAVGADVVFGIPGGAILPAYDPLFdSTRVRHILVRHEQGAGHAAEGYAQATGRVGVCMA 100
                                               89********************************7779******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvt+ia+ay+dsvP+v++tGqva+++iG+dafqe+di Gitlp+tkh+flv++++d+p+++
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 101 TSGPGATNLVTPIADAYMDSVPMVAITGQVASAAIGTDAFQEADICGITLPITKHNFLVQSVDDIPRTI 169
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve....ekvelpgykptvkghklqikkaleliekakkP 203
                                                eaf++a tGrPGPvlvdlPkd+ ++ +++  +     +++lpgy+p +++h++q+++a++li+++++P
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 170 AEAFHLAGTGRPGPVLVDLPKDILQSVTSVLPHeiwpPTLDLPGYRPITRPHNKQVREAAKLISASRRP 238
                                               ***********************9988776555466689****************************** PP

                                 TIGR00118 204 vllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               vl++GgGv++a a +el+ lae++ ipv+ttl+  Gafp+ hp+ lgm GmhG+ +a +a+++adlli+
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 239 VLYIGGGVLKARAAAELRTLAEMTGIPVVTTLMARGAFPDSHPQHLGMPGMHGSVAAVTALQKADLLIT 307
                                               ********************************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke.Wl 340
                                               +Garfddrvtg la+fap+a iih didPaeigkn+++d+pivGd+++v++el+++l +e + e + W+
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 308 LGARFDDRVTGRLASFAPKAAIIHADIDPAEIGKNRTADVPIVGDCREVINELIAALAAEPRPELDaWW 376
                                               ************************************************************9999888** PP

                                 TIGR00118 341 ekieewkkeyilkldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               + ++ w+++y+l +d+  +  ++Pq+vi++l ++   e+i +++vGqhqmwaaqf ++++p ++++sgG
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 377 HTLDGWRRTYPLGYDTPADGsLAPQHVIERLGRISGPETIFAAGVGQHQMWAAQFISYEHPYTWLNSGG 445
                                               *************99865544************************************************ PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               +GtmGf +Paa+Gakv+ p++tv a++Gdg fqm+ qel+t++  +ip+k+ ++nn  lGmv+qWq lf
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 446 AGTMGFAVPAAMGAKVGRPDTTVWAIDGDGCFQMTNQELATCALEGIPIKVAVINNGSLGMVRQWQTLF 514
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklas..........elpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevd 535
                                               y++rys+t+l++           +pdfv+laea+G +g+r  + +e+++ +++a++ + +pv++d++v+
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 515 YDKRYSNTELGThpgsprtgvkRVPDFVRLAEALGCVGLRCDSAAEVDATIEKAMAIDdAPVVVDFVVH 583
                                               ********99752222222222589*****************************998869********* PP

                                 TIGR00118 536 keeevlPmvapGagldel 553
                                                ++ v+Pmva Ga++de+
  lcl|NCBI__GCF_000058485.1:WP_083866922.1 584 PDAMVWPMVAAGASNDEI 601
                                               ***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (621 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: 00:00:00.04
# Mc/sec: 7.75
//
[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