Alignments for a candidate for ilvI in Rhizobium leguminosarum WSM1325

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhizobium leguminosarum WSM1325

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012757472.1 RLEG_RS09710 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000023185.1:WP_012757472.1
          Length = 568

 Score =  528 bits (1361), Expect = e-154
 Identities = 278/557 (49%), Positives = 373/557 (66%), Gaps = 7/557 (1%)

Query: 3   SAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHIL 62
           + E +++  N+ +   M G EI++ AL + GVE+++GYPG AVL IYDE+ +Q   +H L
Sbjct: 2   TGETANSSLNNPSDRRMNGGEIVLQALRDNGVEHIFGYPGAAVLPIYDEIFQQEDIKHFL 61

Query: 63  VRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHA 122
           VRHEQ A HAA+GYAR+TGKVGV LVTSGPGVTNAVT +  A +DS+P+V + G VPT  
Sbjct: 62  VRHEQGAGHAAEGYARSTGKVGVMLVTSGPGVTNAVTALQDALMDSVPLVCLAGQVPTSL 121

Query: 123 IGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSR 182
           IG DAFQECDTVGITRP  KHNFLV+ + DLA TI  AF IAA GRPGPV+VD+PKDV  
Sbjct: 122 IGTDAFQECDTVGITRPCTKHNFLVQHIDDLAKTIHLAFRIAAAGRPGPVLVDMPKDVLF 181

Query: 183 NACKYEYPKSI-DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDEL 239
            +  Y  P  +  + SY P  +G    IR AVAL+  A RP IYTGGG++ A   AS  L
Sbjct: 182 ASGIYVSPDKVGPLPSYQPAMQGDQNAIRSAVALMAEARRPIIYTGGGIINAGPEASRLL 241

Query: 240 RQLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDR 299
           R+   LTG PVT+T+MGLGA+P T   ++ + G  G++EANMA+ +CD++IAIGARFDD 
Sbjct: 242 REFVDLTGFPVTSTIMGLGAYPATGPNWLRVAGQDGSHEANMAIADCDLMIAIGARFDDL 301

Query: 300 VIGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKRE 359
            I     F+  ++K I IDID SSI+KRV VDI I G+   VL ++I   ++    P ++
Sbjct: 302 AISRVHEFSPHSKK-IQIDIDASSINKRVLVDIGIQGDAAHVLADMIHAWRSLSTVPDQK 360

Query: 360 ALAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQ 418
            L  WW QI+ WR+     Y+R    I PQ+ +E++  LTK  D  I +++GQ QMW AQ
Sbjct: 361 RLRAWWLQIDHWRAHQSFSYERLDHAIMPQHALERLHALTKPHDPIIATEIGQ-QMWVAQ 419

Query: 419 FYKFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQY 478
           F+ FD+P RWI SGGLG MG GLP A+G++ A P + V+ I G+ S+Q  ++ELST +Q+
Sbjct: 420 FFGFDKPNRWITSGGLGAMGFGLPAALGVQLANPGRLVIDIAGDASVQTTMKELSTAIQH 479

Query: 479 DTPVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDV 538
             P+KI  L++ + GM R+W ++   +  S SY  +LPDF KLAEAYG VG+R E  +++
Sbjct: 480 QAPIKIFILSDEHPGMAREWGQVPDGSGRSRSYSASLPDFTKLAEAYGAVGLRCESPTEL 539

Query: 539 EPALREAFRLKDRTVFL 555
           +  + E     DR V L
Sbjct: 540 DARIEEMID-TDRPVLL 555


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: 864
Number of extensions: 34
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: 585
Length of database: 568
Length adjustment: 36
Effective length of query: 549
Effective length of database: 532
Effective search space:   292068
Effective search space used:   292068
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_012757472.1 RLEG_RS09710 (acetolactate synthase, large subunit, biosynthetic type)
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.4430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-202  658.4   0.0   5.1e-202  658.1   0.0    1.0  1  lcl|NCBI__GCF_000023185.1:WP_012757472.1  RLEG_RS09710 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_012757472.1  RLEG_RS09710 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.1   0.0  5.1e-202  5.1e-202       1     535 [.      18     560 ..      18     564 .. 0.97

  Alignments for each domain:
  == domain 1  score: 658.1 bits;  conditional E-value: 5.1e-202
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++g+ei++++l+++gve++fGyPG avlpiyd+++ +++++h lvrheq+a haa+Gyar++GkvGv+l
  lcl|NCBI__GCF_000023185.1:WP_012757472.1  18 MNGGEIVLQALRDNGVEHIFGYPGAAVLPIYDEIFqQEDIKHFLVRHEQGAGHAAEGYARSTGKVGVML 86 
                                               789********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vt++ +a +dsvPlv l+Gqv+tsliG+dafqe+d +Git+p+tkh+flv++ +dl+++
  lcl|NCBI__GCF_000023185.1:WP_012757472.1  87 VTSGPGVTNAVTALQDALMDSVPLVCLAGQVPTSLIGTDAFQECDTVGITRPCTKHNFLVQHIDDLAKT 155
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekv.elpgykptvkghklqikkaleliekakkPvl 205
                                               ++ af ia++GrPGPvlvd+Pkdv  a+  +  ++kv  lp+y+p ++g+++ i+ a+ l+++a++P++
  lcl|NCBI__GCF_000023185.1:WP_012757472.1 156 IHLAFRIAAAGRPGPVLVDMPKDVLFASGIYVSPDKVgPLPSYQPAMQGDQNAIRSAVALMAEARRPII 224
                                               ************************999888887766637****************************** PP

                                 TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               + GgG+i a  eas+ l+e+++ +  pvt+t++GlGa+p++ p+ l ++G  G++ean+a+ ++dl+ia
  lcl|NCBI__GCF_000023185.1:WP_012757472.1 225 YTGGGIINAgpEASRLLREFVDLTGFPVTSTIMGLGAYPATGPNWLRVAGQDGSHEANMAIADCDLMIA 293
                                               *******8744699******************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkek 337
                                               +Garfdd   + +++f+p++k i idid ++i+k v vdi i Gda +vl++++++ ++     ++k  
  lcl|NCBI__GCF_000023185.1:WP_012757472.1 294 IGARFDDLAISRVHEFSPHSKKIQIDIDASSINKRVLVDIGIQGDAAHVLADMIHAWRSLstvpDQKRL 362
                                               *******************************************************99888777766666 PP

                                 TIGR00118 338 e.WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404
                                               + W+ +i++w++++ +++++ +++i Pq+ +++l+ l+k  + i++t++Gq qmw+aqf+ ++kp+++i
  lcl|NCBI__GCF_000023185.1:WP_012757472.1 363 RaWWLQIDHWRAHQSFSYERLDHAIMPQHALERLHALTKPhDPIIATEIGQ-QMWVAQFFGFDKPNRWI 430
                                               67***********************************986589*******9.9**************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlG+mGfGlPaalG+++a+p   v++++Gd+s+q +++elst+ + + p+ki il +e+ Gm + W
  lcl|NCBI__GCF_000023185.1:WP_012757472.1 431 TSGGLGAMGFGLPAALGVQLANPGRLVIDIAGDASVQTTMKELSTAIQHQAPIKIFILSDEHPGMAREW 499
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevd 535
                                                ++      s+++ as lpdf+klaeayG++g+r e+p el+++++e++ +++pvll  +v+
  lcl|NCBI__GCF_000023185.1:WP_012757472.1 500 GQVPDGSGRSRSYSAS-LPDFTKLAEAYGAVGLRCESPTELDARIEEMIDTDRPVLLHCRVA 560
                                               *************995.****************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (568 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 0.02s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 8.08
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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