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_004142414.1 Mesci_3241 acetolactate synthase large subunit

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



>NCBI__GCF_000185905.1:YP_004142414.1
          Length = 593

 Score =  638 bits (1646), Expect = 0.0
 Identities = 318/569 (55%), Positives = 422/569 (74%), Gaps = 6/569 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM GAE++V AL + GV++V+GYPGGAVL IYDE+ +Q + EHILVRHEQ A HAA+GYA
Sbjct: 10  EMTGAEMVVQALKDNGVQHVFGYPGGAVLPIYDEIFQQDEVEHILVRHEQGAGHAAEGYA 69

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TNAVT +  A +DSIP+V +TG VPT  IG DAFQECDTVGIT
Sbjct: 70  RSTGKAGVMLVTSGPGATNAVTPLQDALMDSIPLVCLTGQVPTSLIGSDAFQECDTVGIT 129

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKDV +LAATI +AF +A TGRPGPVVVDIPKDV      Y  P+     S
Sbjct: 130 RPCTKHNWLVKDVNELAATIHEAFHVATTGRPGPVVVDIPKDVQFAKGFYVPPQIAPRTS 189

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  +G   +I+ AV L+ GA++P IY+GGGV+ +   AS  LR+L  LTG P+T+TLM
Sbjct: 190 YQPKVQGDLEKIKAAVELMAGAKKPIIYSGGGVINSGPEASHLLRELVDLTGFPITSTLM 249

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P + K ++GMLGMHGTYEANMAM +CDV+I IGARFDDR+ G    F+  ++K I
Sbjct: 250 GLGAYPASGKNWMGMLGMHGTYEANMAMHDCDVMICIGARFDDRITGRLTAFSPNSKK-I 308

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K V  ++PI+G+V  VL++++   +AS  K  ++AL  WWEQI +WR+ D
Sbjct: 309 HIDIDPSSINKNVHTEVPIIGDVGRVLEDMVRLWRAS-AKADKKALYPWWEQIAKWRARD 367

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
            L Y  ++++I PQY +E+++ELTKG D +I ++VGQHQMWAAQ Y+ ++P RW+ SGGL
Sbjct: 368 SLAYKMNNDVIMPQYAIERLYELTKGMDTYITTEVGQHQMWAAQHYRVEKPNRWMTSGGL 427

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G++ A P+  V+ I G+ S+QM +QE+S  +Q++ P+KI  LNN Y+GM
Sbjct: 428 GTMGYGLPAALGVQIAHPDALVIDIAGDASVQMTMQEMSAAVQHNAPIKIFILNNQYMGM 487

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQ++ + NR SHSY +A+PDFVKLAEAYG  G+R EK  +++ A++E   ++ + V 
Sbjct: 488 VRQWQQLLHGNRLSHSYTEAMPDFVKLAEAYGGHGIRCEKPDELDDAIKEMISVR-KPVL 546

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAE 583
            D +     N +PM+ +GK  +EMLL  E
Sbjct: 547 FDCRVATLANCFPMIPSGKAHNEMLLPDE 575


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: 952
Number of extensions: 39
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: 593
Length adjustment: 37
Effective length of query: 548
Effective length of database: 556
Effective search space:   304688
Effective search space used:   304688
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_004142414.1 Mesci_3241 (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.19519.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-247  807.7   0.7   2.9e-247  807.5   0.7    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004142414.1  Mesci_3241 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004142414.1  Mesci_3241 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  807.5   0.7  2.9e-247  2.9e-247       1     555 [.      11     572 ..      11     574 .. 0.98

  Alignments for each domain:
  == domain 1  score: 807.5 bits;  conditional E-value: 2.9e-247
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gae++v++lk++gv++vfGyPGGavlpiyd+++ ++e+ehilvrheq+a haa+Gyar++Gk+Gv+l
  lcl|NCBI__GCF_000185905.1:YP_004142414.1  11 MTGAEMVVQALKDNGVQHVFGYPGGAVLPIYDEIFqQDEVEHILVRHEQGAGHAAEGYARSTGKAGVML 79 
                                               79*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vt++ +a +ds+Plv ltGqv+tsliGsdafqe+d +Git+p+tkh++lvk++++l+++
  lcl|NCBI__GCF_000185905.1:YP_004142414.1  80 VTSGPGATNAVTPLQDALMDSIPLVCLTGQVPTSLIGSDAFQECDTVGITRPCTKHNWLVKDVNELAAT 148
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               ++eaf++a+tGrPGPv+vd+Pkdv+ a+  +  ++     +y+p+v+g+  +ik+a+el++ akkP+++
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 149 IHEAFHVATTGRPGPVVVDIPKDVQFAKGFYVPPQIAPRTSYQPKVQGDLEKIKAAVELMAGAKKPIIY 217
                                               ****************************999999999999***************************** PP

                                 TIGR00118 207 vGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                                GgGvi +  eas+ l+el++ +  p+t+tl+GlGa+p+  ++ +gmlGmhGt+ean+a++++d++i++
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 218 SGGGVINSgpEASHLLRELVDLTGFPITSTLMGLGAYPASGKNWMGMLGMHGTYEANMAMHDCDVMICI 286
                                               ******87446999******************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee...ekkeke. 338
                                               Garfddr+tg l+ f+p++k ihididP++i+knv++++pi+Gd+ +vle++++  ++    +kk    
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 287 GARFDDRITGRLTAFSPNSKKIHIDIDPSSINKNVHTEVPIIGDVGRVLEDMVRLWRASakaDKKALYp 355
                                               *****************************************************9888774333444448 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfits 406
                                               W+e+i++w+++  l+++ +++ i Pq+ i++l++l+k+ ++++tt+vGqhqmwaaq+y+++kp++++ts
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 356 WWEQIAKWRARDSLAYKMNNDVIMPQYAIERLYELTKGmDTYITTEVGQHQMWAAQHYRVEKPNRWMTS 424
                                               *************************************999***************************** PP

                                 TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                               gGlGtmG+GlPaalG+++a+p++ v++++Gd+s+qm++qe+s++v+ + p+ki ilnn+++Gmv+qWq+
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 425 GGLGTMGYGLPAALGVQIAHPDALVIDIAGDASVQMTMQEMSAAVQHNAPIKIFILNNQYMGMVRQWQQ 493
                                               ********************************************************************* PP

                                 TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmv 544
                                               l++ +r s+++ ++ +pdfvklaeayG +gir ekp+el++++ke++++++pvl+d +v++ ++++Pm+
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 494 LLHGNRLSHSYTEA-MPDFVKLAEAYGGHGIRCEKPDELDDAIKEMISVRKPVLFDCRVATLANCFPMI 561
                                               *************5.****************************************************** PP

                                 TIGR00118 545 apGagldelve 555
                                               ++G++ +e++ 
  lcl|NCBI__GCF_000185905.1:YP_004142414.1 562 PSGKAHNEMLL 572
                                               ********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (593 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: 8.50
//
[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