Alignments for a candidate for ilvI in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Caulobacter crescentus NA1000

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate CCNA_02185 CCNA_02185 acetolactate synthase large subunit

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



>FitnessBrowser__Caulo:CCNA_02185
          Length = 601

 Score =  662 bits (1707), Expect = 0.0
 Identities = 332/572 (58%), Positives = 422/572 (73%), Gaps = 7/572 (1%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78
           M GAEI+V  L ++GVE ++GYPGGAVL IYD L  + + +HILVRHEQ A HAA+GYAR
Sbjct: 20  MTGAEIVVRGLVDQGVEVLFGYPGGAVLPIYDALFHEPRLQHILVRHEQGAAHAAEGYAR 79

Query: 79  ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138
           ++GK GV LVTSGPG TNA+TGI  A +DSIPMVVITG VPTH IG DAFQE DTVG+TR
Sbjct: 80  SSGKPGVVLVTSGPGATNAITGIMDALMDSIPMVVITGQVPTHLIGTDAFQEADTVGMTR 139

Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSI-DMRS 197
              KHN+LVKDVRDL   I +AF IA TGRPGPV++DIPKDV     +Y  P  +    +
Sbjct: 140 SCTKHNYLVKDVRDLPQIIHEAFKIATTGRPGPVLIDIPKDVQFAKGEYFGPGEVASTHA 199

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  KG +G+I +A  ++  A RP  YTGGGV+ A   AS  LR+ AALTG PVT+TLM
Sbjct: 200 YAPRTKGDAGRIAEAARMIAQARRPIFYTGGGVINAGPKASAALREFAALTGAPVTSTLM 259

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGAFP     ++GMLGMHGT+EAN AM +CDV+I +GARFDDRV G    F+  ++K I
Sbjct: 260 GLGAFPAADPAWLGMLGMHGTFEANNAMHDCDVMICVGARFDDRVTGRLDAFSPGSKK-I 318

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K V+VD+PIVG+   VL++LIA  KA++++P + AL  WW QI+QWR+  
Sbjct: 319 HIDIDPSSINKNVRVDLPIVGDAGSVLEDLIAAWKAANLQPNKAALTDWWAQIDQWRARQ 378

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CL Y RS  +IKPQY +E+++ELTK  D +I ++VGQHQMWAAQF++F+EP RW+ SGGL
Sbjct: 379 CLSYRRSDSVIKPQYAIERLYELTKDKDVYITTEVGQHQMWAAQFFRFEEPNRWMTSGGL 438

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G++ A P   VV I GE SIQMCIQELST +Q+D PVKI  LNN ++GM
Sbjct: 439 GTMGYGLPAALGVQLAHPNSLVVDIAGEASIQMCIQELSTAIQFDLPVKIFILNNEWMGM 498

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQ++ +  RYSHSY D+LPDFVKLAEAYG VG+R +  ++++  + E     D+ V 
Sbjct: 499 VRQWQQLLHGERYSHSYSDSLPDFVKLAEAYGAVGIRCDNPAELDAKILEMVN-SDKPVI 557

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLG-AEDL 585
            D + +  EN  PM+ +GK  +EM++G  ED+
Sbjct: 558 FDCRVEKHENCLPMIPSGKAHNEMIMGEVEDI 589


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: 1021
Number of extensions: 41
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: 601
Length adjustment: 37
Effective length of query: 548
Effective length of database: 564
Effective search space:   309072
Effective search space used:   309072
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 CCNA_02185 CCNA_02185 (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.3326320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-251  821.6   0.0   1.8e-251  821.4   0.0    1.0  1  FitnessBrowser__Caulo:CCNA_02185  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_02185  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  821.4   0.0  1.8e-251  1.8e-251       1     555 [.      20     583 ..      20     585 .. 0.97

  Alignments for each domain:
  == domain 1  score: 821.4 bits;  conditional E-value: 1.8e-251
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       ++gaei+v+ l ++gve++fGyPGGavlpiydal+ +  l+hilvrheq+aahaa+Gyar+sGk+Gvvl+tsGPGat
  FitnessBrowser__Caulo:CCNA_02185  20 MTGAEIVVRGLVDQGVEVLFGYPGGAVLPIYDALFhEPRLQHILVRHEQGAAHAAEGYARSSGKPGVVLVTSGPGAT 96 
                                       79********************************97899************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       n++tgi +a +ds+P+vv+tGqv+t+liG+dafqe+d +G+t+++tkh++lvk+++dlp+i++eaf+ia+tGrPGPv
  FitnessBrowser__Caulo:CCNA_02185  97 NAITGIMDALMDSIPMVVITGQVPTHLIGTDAFQEADTVGMTRSCTKHNYLVKDVRDLPQIIHEAFKIATTGRPGPV 173
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..easeelkelaerl 227
                                       l+d+Pkdv+ a+ e+  + e  +  +y+p++kg+  +i++a+ +i++a++P+ + GgGvi a  +as+ l+e+a  +
  FitnessBrowser__Caulo:CCNA_02185 174 LIDIPKDVQFAKGEYFGPgEVASTHAYAPRTKGDAGRIAEAARMIAQARRPIFYTGGGVINAgpKASAALREFAALT 250
                                       **************99994556789***********************************88346999********* PP

                         TIGR00118 228 kipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaei 304
                                        +pvt+tl+GlGafp+ +p  lgmlGmhGt ean a++++d++i+vGarfddrvtg l+ f+p +k ihididP++i
  FitnessBrowser__Caulo:CCNA_02185 251 GAPVTSTLMGLGAFPAADPAWLGMLGMHGTFEANNAMHDCDVMICVGARFDDRVTGRLDAFSPGSKKIHIDIDPSSI 327
                                       ***************************************************************************** PP

                         TIGR00118 305 gknvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkd 376
                                       +knv+vd+pivGda +vle+l+++ k+     +k     W+++i++w+++++l++ ++++ ikPq+ i++l++l+kd
  FitnessBrowser__Caulo:CCNA_02185 328 NKNVRVDLPIVGDAGSVLEDLIAAWKAAnlqpNKAALTdWWAQIDQWRARQCLSYRRSDSVIKPQYAIERLYELTKD 404
                                       **********************99887767663333335*************************************9 PP

                         TIGR00118 377 .eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstive 452
                                        ++++tt+vGqhqmwaaqf+++++p++++tsgGlGtmG+GlPaalG+++a+p++ vv+++G++s+qm +qelst+ +
  FitnessBrowser__Caulo:CCNA_02185 405 kDVYITTEVGQHQMWAAQFFRFEEPNRWMTSGGLGTMGYGLPAALGVQLAHPNSLVVDIAGEASIQMCIQELSTAIQ 481
                                       89*************************************************************************** PP

                         TIGR00118 453 ydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvl 529
                                       +d+pvki ilnne++Gmv+qWq+l++ erys+++  s lpdfvklaeayG++gir  +p+el++k+ e+++s++pv+
  FitnessBrowser__Caulo:CCNA_02185 482 FDLPVKIFILNNEWMGMVRQWQQLLHGERYSHSYSDS-LPDFVKLAEAYGAVGIRCDNPAELDAKILEMVNSDKPVI 557
                                       ***********************************95.*************************************** PP

                         TIGR00118 530 ldvevdkeeevlPmvapGagldelve 555
                                       +d +v+k+e++lPm+++G++ +e++ 
  FitnessBrowser__Caulo:CCNA_02185 558 FDCRVEKHENCLPMIPSGKAHNEMIM 583
                                       ************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (601 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 17.23
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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