Alignments for a candidate for ilvI in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Novosphingobium aromaticivorans DSM 12444

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011445904.1 SARO_RS11375 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_000013325.1:WP_011445904.1
          Length = 582

 Score =  570 bits (1468), Expect = e-167
 Identities = 299/571 (52%), Positives = 391/571 (68%), Gaps = 7/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E  GAEILV +L  +GVE+V+GYPGGAVL IYD L    +  HILVRHE  A HAA+GYA
Sbjct: 4   ERSGAEILVESLVAKGVEFVFGYPGGAVLPIYDALFGDERLRHILVRHEAGAAHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPG TNAVTGIA A++DSIPMVVITG VPT  IG DAFQE DT+GIT
Sbjct: 64  RATGKPGVVLVTSGPGATNAVTGIADAFMDSIPMVVITGQVPTALIGSDAFQEADTIGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHN+LVKD   LAATI +AF IA  GRPGPVV+DIPKDV      +          
Sbjct: 124 RHCTKHNYLVKDPSQLAATIDEAFRIATEGRPGPVVIDIPKDVQIATAAWSSAAPQQRNR 183

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  +G + +I +A+ L+  A+ P  YTGGGV+ A   A+  LR+L +LTG PVT+TLM
Sbjct: 184 YAPQTEGGAKEIAEAIELIAKAKAPVFYTGGGVINAGPEAARLLRELQSLTGAPVTSTLM 243

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGAFP     ++GMLGMHGTYEANM M   D+++ IGARFDDRV G    F+  ++K I
Sbjct: 244 GLGAFPADHPAWLGMLGMHGTYEANMTMNRADLVVCIGARFDDRVTGRLDAFSPNSKK-I 302

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDID +SI+K V+VD+P++G+   VL +LI          +++ L +W  +I+ WR+  
Sbjct: 303 HIDIDRASINKTVQVDLPVIGDCGKVLAQLIEAWLERGY--QKQDLTEWNARIDGWRARQ 360

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
            L + R  + I PQ  +E+++ELT+  +  I ++VGQHQMWAAQ + F +P +W+ SGGL
Sbjct: 361 SLAFPRRGKEIMPQLAIERLYELTRHKEPIISTEVGQHQMWAAQHFHFMKPNKWLTSGGL 420

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G +  FP+  V+ I G+ SIQM IQEL T  QY  PVK+  LNN ++GM
Sbjct: 421 GTMGYGLPAAIGAQAGFPDALVIDIAGDASIQMNIQELGTATQYRLPVKVFVLNNEWMGM 480

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ Y++RYS+SY D+LPDFVKLAEAYG  G+R+   S+++  + +A    D  VF
Sbjct: 481 VRQWQELTYESRYSNSYSDSLPDFVKLAEAYGWKGIRITDESELDAGI-QAMIDHDGPVF 539

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           +D       N +PM+ +G   ++M+L  +++
Sbjct: 540 VDCLVAKEANCFPMIPSGAAHTDMILYGDEV 570


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: 905
Number of extensions: 38
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: 582
Length adjustment: 36
Effective length of query: 549
Effective length of database: 546
Effective search space:   299754
Effective search space used:   299754
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_011445904.1 SARO_RS11375 (biosynthetic-type 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.875149.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-243  793.4   0.0   6.1e-243  793.2   0.0    1.0  1  NCBI__GCF_000013325.1:WP_011445904.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013325.1:WP_011445904.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.2   0.0  6.1e-243  6.1e-243       2     555 ..       6     565 ..       5     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 793.2 bits;  conditional E-value: 6.1e-243
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +gaeilvesl ++gve vfGyPGGavlpiydal+ d+ l+hilvrhe +aahaa+Gyara+Gk+Gvvl+tsGP
  NCBI__GCF_000013325.1:WP_011445904.1   6 SGAEILVESLVAKGVEFVFGYPGGAVLPIYDALFgDERLRHILVRHEAGAAHAAEGYARATGKPGVVLVTSGP 78 
                                           79********************************9999*********************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Gatn+vtgia+a++ds+P+vv+tGqv+t+liGsdafqe+d +Git+ +tkh++lvk++++l++++ eaf ia+
  NCBI__GCF_000013325.1:WP_011445904.1  79 GATNAVTGIADAFMDSIPMVVITGQVPTALIGSDAFQEADTIGITRHCTKHNYLVKDPSQLAATIDEAFRIAT 151
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..eas 217
                                            GrPGPv++d+Pkdv+ a+   +  +  +   y+p+++g  + i++a+eli+kak Pv + GgGvi a  ea 
  NCBI__GCF_000013325.1:WP_011445904.1 152 EGRPGPVVIDIPKDVQIATAAWSSAAPQQRNRYAPQTEGGAKEIAEAIELIAKAKAPVFYTGGGVINAgpEAA 224
                                           *************************9999*************************************8844689 PP

                             TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap 290
                                           + l+el   + +pvt+tl+GlGafp+dhp  lgmlGmhGt+ean++++ adl++++Garfddrvtg l+ f+p
  NCBI__GCF_000013325.1:WP_011445904.1 225 RLLRELQSLTGAPVTSTLMGLGAFPADHPAWLGMLGMHGTYEANMTMNRADLVVCIGARFDDRVTGRLDAFSP 297
                                           99*********************************************************************** PP

                             TIGR00118 291 eakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wlekieewkkeyilkldeeees 360
                                           ++k ihidid a+i+k+v+vd+p++Gd+ kvl++l+++  e+  +k++   W ++i+ w++++ l++ ++ ++
  NCBI__GCF_000013325.1:WP_011445904.1 298 NSKKIHIDIDRASINKTVQVDLPVIGDCGKVLAQLIEAWLERgyQKQDLTeWNARIDGWRARQSLAFPRRGKE 370
                                           *************************************99888776666556********************** PP

                             TIGR00118 361 ikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvv 432
                                           i Pq  i++l++l+++ e i++t+vGqhqmwaaq++++ kp+k++tsgGlGtmG+GlPaa+Ga+ + p++ v+
  NCBI__GCF_000013325.1:WP_011445904.1 371 IMPQLAIERLYELTRHkEPIISTEVGQHQMWAAQHFHFMKPNKWLTSGGLGTMGYGLPAAIGAQAGFPDALVI 443
                                           *************987689****************************************************** PP

                             TIGR00118 433 avtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkg 505
                                           +++Gd+s+qmn+qel t+++y +pvk+ +lnne++Gmv+qWqel ye rys+++  s lpdfvklaeayG kg
  NCBI__GCF_000013325.1:WP_011445904.1 444 DIAGDASIQMNIQELGTATQYRLPVKVFVLNNEWMGMVRQWQELTYESRYSNSYSDS-LPDFVKLAEAYGWKG 515
                                           *******************************************************95.*************** PP

                             TIGR00118 506 iriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                           iri++++el++ ++ ++ +++pv++d  v+ke++++Pm+++Ga+ ++++ 
  NCBI__GCF_000013325.1:WP_011445904.1 516 IRITDESELDAGIQAMIDHDGPVFVDCLVAKEANCFPMIPSGAAHTDMIL 565
                                           ***********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (582 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: 30.50
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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