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.3506026.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 37.66
//
[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:

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:

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:

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:

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