Alignments for a candidate for ilvI in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sphingomonas wittichii RW1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011951457.1 SWIT_RS03100 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000016765.1:WP_011951457.1
          Length = 584

 Score =  587 bits (1513), Expect = e-172
 Identities = 310/573 (54%), Positives = 395/573 (68%), Gaps = 9/573 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM GA+IL+ AL + GVE V+GYPGGAVL IYD L KQ +  HILVRHE  AVHAA+GYA
Sbjct: 4   EMTGADILIQALNDLGVEVVFGYPGGAVLPIYDALFKQNRIRHILVRHEAGAVHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TNAVTGIA A LDSIP+VV+TG V T  IG DAFQECDTVGIT
Sbjct: 64  RSTGKPGVVLVTSGPGATNAVTGIADALLDSIPLVVLTGQVGTPLIGSDAFQECDTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYP--KSIDM 195
           R   KHN+LVKD   L   I +AF IA +GRPGPVVVD+PKDV   +  Y  P  +++  
Sbjct: 124 RHCTKHNYLVKDPALLGDVIHEAFHIATSGRPGPVVVDLPKDVQVASAAYRKPSVQALPH 183

Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNT 253
           + Y P  K     I +AVA++  AERP +YTGGG++ A   AS  LR+LA +TG PVT+T
Sbjct: 184 KGYRPQVKADPTLIEQAVAMIAAAERPILYTGGGIINAGPLASQVLRELARVTGAPVTST 243

Query: 254 LMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARK 313
           LMGLGAFP +S Q++GMLGMHGTYEANMAM   D+++ +GARFDDRV G    F   ++K
Sbjct: 244 LMGLGAFPASSGQWLGMLGMHGTYEANMAMNKADLIVCLGARFDDRVTGRLDAFAPHSKK 303

Query: 314 IIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRS 373
            IH+DID SSI+K V+ DI IVG+V   +++++   KA   + +   LA W+EQI+ WR+
Sbjct: 304 -IHVDIDRSSINKIVRADIGIVGDVGRAMEDMVKIWKAG--QHQARDLAAWYEQIDAWRA 360

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432
              LK+  S++ I PQ  + K+WE T      I ++VGQHQMWAAQ + F+ P +W+ SG
Sbjct: 361 RKSLKFPASTKEIMPQLAIRKLWEATHALKPIITTEVGQHQMWAAQHFDFEGPNKWLTSG 420

Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492
           GLGTMG GLP A+G +   P   V+ I GE SIQM IQEL T  QY  PVK+  LNN Y+
Sbjct: 421 GLGTMGYGLPAAIGAQLGNPNALVIDIAGEASIQMNIQELGTATQYRLPVKVFILNNEYM 480

Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552
           GMVRQWQ++ Y  RYS SY DALPDFVKLAEAYG  G+ +EK  +++  +  A    D  
Sbjct: 481 GMVRQWQDLTYAGRYSQSYSDALPDFVKLAEAYGWKGVLIEKPEELDAGI-AAMLEHDGP 539

Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           V +D +     N +PM+ +G   ++M+L A+++
Sbjct: 540 VIVDCRVAKLANCFPMIPSGAAHTDMILEADEV 572


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: 969
Number of extensions: 44
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: 584
Length adjustment: 37
Effective length of query: 548
Effective length of database: 547
Effective search space:   299756
Effective search space used:   299756
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_011951457.1 SWIT_RS03100 (acetolactate synthase 3 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.9703.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-238  778.1   0.4   2.7e-238  777.8   0.4    1.0  1  lcl|NCBI__GCF_000016765.1:WP_011951457.1  SWIT_RS03100 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_011951457.1  SWIT_RS03100 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  777.8   0.4  2.7e-238  2.7e-238       1     555 [.       5     567 ..       5     569 .. 0.97

  Alignments for each domain:
  == domain 1  score: 777.8 bits;  conditional E-value: 2.7e-238
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga+il+++l++ gve+vfGyPGGavlpiydal+ ++ ++hilvrhe +a+haa+Gyar++Gk+Gvvl
  lcl|NCBI__GCF_000016765.1:WP_011951457.1   5 MTGADILIQALNDLGVEVVFGYPGGAVLPIYDALFkQNRIRHILVRHEAGAVHAAEGYARSTGKPGVVL 73 
                                               79*********************************8999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtgia+a lds+PlvvltGqv t liGsdafqe+d +Git+ +tkh++lvk+++ l  +
  lcl|NCBI__GCF_000016765.1:WP_011951457.1  74 VTSGPGATNAVTGIADALLDSIPLVVLTGQVGTPLIGSDAFQECDTVGITRHCTKHNYLVKDPALLGDV 142
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204
                                               ++eaf+ia++GrPGPv+vdlPkdv+ a+  ++++  + +  +gy+p+vk++++ i++a+ +i++a++P+
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 143 IHEAFHIATSGRPGPVVVDLPKDVQVASAAYRKPsvQALPHKGYRPQVKADPTLIEQAVAMIAAAERPI 211
                                               *************************99999988844666677*************************** PP

                                 TIGR00118 205 llvGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                               l+ GgG+i a+  as+ l+ela  + +pvt+tl+GlGafp+   + lgmlGmhGt+ean+a+++adl++
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 212 LYTGGGIINAGplASQVLRELARVTGAPVTSTLMGLGAFPASSGQWLGMLGMHGTYEANMAMNKADLIV 280
                                               ********9976689****************************************************** PP

                                 TIGR00118 272 avGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke 338
                                               ++Garfddrvtg l+ fap++k ih+did ++i+k+v++di ivGd+ + +e+++k  k+   + ++  
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 281 CLGARFDDRVTGRLDAFAPHSKKIHVDIDRSSINKIVRADIGIVGDVGRAMEDMVKIWKAGqhQARDLA 349
                                               ******************************************************997665533667777 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405
                                                W+e+i+ w++++ lk+  + ++i Pq  i++l++ ++  + i+tt+vGqhqmwaaq+++++ p+k++t
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 350 aWYEQIDAWRARKSLKFPASTKEIMPQLAIRKLWEATHAlKPIITTEVGQHQMWAAQHFDFEGPNKWLT 418
                                               8***********************************998899*************************** PP

                                 TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                               sgGlGtmG+GlPaa+Ga++++p++ v++++G++s+qmn+qel t+++y +pvk+ ilnne++Gmv+qWq
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 419 SGGLGTMGYGLPAAIGAQLGNPNALVIDIAGEASIQMNIQELGTATQYRLPVKVFILNNEYMGMVRQWQ 487
                                               ********************************************************************* PP

                                 TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543
                                               +l y +rys+++  + lpdfvklaeayG kg+ iekpeel++ ++ +le+++pv++d +v+k ++++Pm
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 488 DLTYAGRYSQSYSDA-LPDFVKLAEAYGWKGVLIEKPEELDAGIAAMLEHDGPVIVDCRVAKLANCFPM 555
                                               *************95.***************************************************** PP

                                 TIGR00118 544 vapGagldelve 555
                                               +++Ga+ ++++ 
  lcl|NCBI__GCF_000016765.1:WP_011951457.1 556 IPSGAAHTDMIL 567
                                               **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (584 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.04
//
[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