Alignments for a candidate for ilvI in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Mesorhizobium ciceri WSM1271

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate YP_004142386.1 Mesci_3212 acetolactate synthase large subunit

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



>NCBI__GCF_000185905.1:YP_004142386.1
          Length = 594

 Score =  609 bits (1571), Expect = e-179
 Identities = 304/574 (52%), Positives = 410/574 (71%), Gaps = 6/574 (1%)

Query: 14  SAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAA 73
           +A+  M GAEI++HAL + GVE+V+GYPG A+L IYDE+ +Q   +HILVRHEQ A HAA
Sbjct: 9   TASKRMTGAEIVLHALRDNGVEHVFGYPGAALLPIYDEIFQQDDIKHILVRHEQGAGHAA 68

Query: 74  DGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDT 133
           +GYAR+TGKVGV LVTSGPG TNAVT +  A +DS+P+V +TG VPT  IG DAFQECDT
Sbjct: 69  EGYARSTGKVGVMLVTSGPGTTNAVTPLQDALMDSVPIVCLTGQVPTTLIGSDAFQECDT 128

Query: 134 VGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPK-S 192
           VGITRP  KHN LVKDV +LA+TI +AF IA +GRPGPV+VD+PKDV      Y  P  +
Sbjct: 129 VGITRPCTKHNSLVKDVNELASTIHRAFHIAKSGRPGPVLVDMPKDVLFATGVYTPPSDA 188

Query: 193 IDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPV 250
             ++S  P  +    +I KA+ L+  A RP IYTGGG+V +   AS  LR+L  LT  P+
Sbjct: 189 AALKSCRPTVESDINEIGKAIELMANARRPVIYTGGGIVNSGMEASRLLRELVELTDFPI 248

Query: 251 TNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQ 310
           T+TLMGLGA+P + K ++ M+G+HG+YEANMAM  CDV++ IGARFDDRV      F+  
Sbjct: 249 TSTLMGLGAYPASGKNWLKMVGLHGSYEANMAMHECDVMLCIGARFDDRVTSRVEAFSPN 308

Query: 311 ARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQ 370
           +RK IH+DIDPSSI+K V+ D+ I G+   V+  L+   +A    P R  + +WW++I +
Sbjct: 309 SRK-IHVDIDPSSINKTVRADVGIQGDAGKVVDSLVRSWRALPQNPDRRRIDEWWKKIAR 367

Query: 371 WRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWI 429
           WR  +   Y+ S+E+I PQY VE+++ LTK  D +I ++VGQHQ+WAAQFY F++PRRW+
Sbjct: 368 WRGRNSFSYEMSNEVIMPQYAVERLYALTKDRDTYITTEVGQHQIWAAQFYGFEKPRRWM 427

Query: 430 NSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNN 489
            SGGLGTMG GLP A+G++ A PE  V+ I G+ S+QM ++E+S  +QY+ P+KI  LNN
Sbjct: 428 TSGGLGTMGYGLPAALGVQIAHPESLVIDIAGDASVQMTMKEMSAAVQYNAPIKIFILNN 487

Query: 490 GYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLK 549
            Y+GMVRQWQ++ + NR +HSY + LPDFVKLAEA+G VG+R EK +D++ A++E   + 
Sbjct: 488 SYMGMVRQWQQMLHGNRLAHSYSETLPDFVKLAEAFGAVGIRCEKPADLDDAIQEMIDV- 546

Query: 550 DRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583
           +R V  D +     N  PM++ G+  +EMLL  E
Sbjct: 547 NRPVLFDCRVAELANCLPMIRTGRAHNEMLLPGE 580


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: 923
Number of extensions: 40
Number of successful extensions: 6
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: 594
Length adjustment: 37
Effective length of query: 548
Effective length of database: 557
Effective search space:   305236
Effective search space used:   305236
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 YP_004142386.1 Mesci_3212 (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.21259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-235  767.1   0.0   6.2e-235  766.8   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004142386.1  Mesci_3212 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004142386.1  Mesci_3212 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.8   0.0  6.2e-235  6.2e-235       1     554 [.      14     576 ..      14     578 .. 0.97

  Alignments for each domain:
  == domain 1  score: 766.8 bits;  conditional E-value: 6.2e-235
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gaei++++l+++gve+vfGyPG a+lpiyd+++ +++++hilvrheq+a haa+Gyar++GkvGv+l
  lcl|NCBI__GCF_000185905.1:YP_004142386.1  14 MTGAEIVLHALRDNGVEHVFGYPGAALLPIYDEIFqQDDIKHILVRHEQGAGHAAEGYARSTGKVGVML 82 
                                               79*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG+tn+vt++ +a +dsvP+v ltGqv+t+liGsdafqe+d +Git+p+tkh+ lvk++++l+++
  lcl|NCBI__GCF_000185905.1:YP_004142386.1  83 VTSGPGTTNAVTPLQDALMDSVPIVCLTGQVPTTLIGSDAFQECDTVGITRPCTKHNSLVKDVNELAST 151
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvl 205
                                               +++af+ia++GrPGPvlvd+Pkdv  a+  ++ + +   l++ +ptv+++ + i ka+el+++a++Pv+
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 152 IHRAFHIAKSGRPGPVLVDMPKDVLFATGVYTPPsDAAALKSCRPTVESDINEIGKAIELMANARRPVI 220
                                               ************************998887776658899****************************** PP

                                 TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272
                                               + GgG++ +  eas+ l+el+e ++ p+t+tl+GlGa+p+  ++ l m+G+hG++ean+a++e+d++++
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 221 YTGGGIVNSgmEASRLLRELVELTDFPITSTLMGLGAYPASGKNWLKMVGLHGSYEANMAMHECDVMLC 289
                                               *******8734699******************************************************* PP

                                 TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkek 337
                                               +Garfddrvt+ ++ f+p+++ ih+didP++i+k+v++d+ i Gda kv++ l++  ++     +++ +
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 290 IGARFDDRVTSRVEAFSPNSRKIHVDIDPSSINKTVRADVGIQGDAGKVVDSLVRSWRALpqnpDRRRI 358
                                               ******************************************************998887766644444 PP

                                 TIGR00118 338 e.WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404
                                               + W++ki++w+ ++ ++++ ++e i Pq+ +++l+ l+kd ++++tt+vGqhq+waaqfy ++kpr+++
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 359 DeWWKKIARWRGRNSFSYEMSNEVIMPQYAVERLYALTKDrDTYITTEVGQHQIWAAQFYGFEKPRRWM 427
                                               45*************************************999*************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlGtmG+GlPaalG+++a+pe+ v++++Gd+s+qm+++e+s++v+y+ p+ki ilnn+++Gmv+qW
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 428 TSGGLGTMGYGLPAALGVQIAHPESLVIDIAGDASVQMTMKEMSAAVQYNAPIKIFILNNSYMGMVRQW 496
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q++++ +r ++++ ++ lpdfvklaea+G++gir ekp++l+++++e++ +++pvl+d +v++ +++lP
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 497 QQMLHGNRLAHSYSET-LPDFVKLAEAFGAVGIRCEKPADLDDAIQEMIDVNRPVLFDCRVAELANCLP 564
                                               *************995.**************************************************** PP

                                 TIGR00118 543 mvapGagldelv 554
                                               m+ +G + +e++
  lcl|NCBI__GCF_000185905.1:YP_004142386.1 565 MIRTGRAHNEML 576
                                               **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (594 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: 11.09
//
[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