Alignments for a candidate for ilvI in Novosphingobium barchaimii LL02

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Novosphingobium barchaimii LL02

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_059150772.1 V474_RS04395 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_001046635.1:WP_059150772.1
          Length = 580

 Score =  557 bits (1435), Expect = e-163
 Identities = 290/571 (50%), Positives = 389/571 (68%), Gaps = 9/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E  GA ILV +L  +GVE+V+GYPGGAVL IYD L    +  HILVRHE  A HAA+GYA
Sbjct: 4   ERSGANILVESLVRQGVEFVFGYPGGAVLPIYDALFGDERLRHILVRHEAGAGHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TN +T IA A+LDSIP+VVITG VPT  IG D FQE DTVGI+
Sbjct: 64  RSTGKPGVVLVTSGPGATNVITAIADAFLDSIPLVVITGQVPTALIGSDGFQEADTVGIS 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHN+LVKD  +LAA I +AF IA TGRPGPV++DIPKDV   +  +    +   + 
Sbjct: 124 RHCTKHNYLVKDPAELAAVIDEAFQIATTGRPGPVLIDIPKDVQIASAAWNDGPTQRRQR 183

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

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGAFP     ++GMLGMHGTYEAN+AM   D+++ +GARFDDRV G    F   ++K I
Sbjct: 244 GLGAFPADHADWLGMLGMHGTYEANLAMNQADLIVCVGARFDDRVTGRLDAFAPNSKK-I 302

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDID SSI+K V+V++PIVG+   VL++++A+  +     K + L +W  +++ WR   
Sbjct: 303 HIDIDRSSINKIVRVELPIVGDCAVVLEQMLAEWGSR----KGQDLTEWKARVDTWREKK 358

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
            L +  + + I PQ  +++++ELTK  D  I ++VGQHQMWAAQ + F  P +W+ SGGL
Sbjct: 359 SLSFPLNDDAIMPQLAIQRLFELTKDKDPIISTEVGQHQMWAAQHFPFFSPNKWLTSGGL 418

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG GLP A+G +   P+  V+ I G+ SIQM IQEL T  QY  PVK+  LNN ++GM
Sbjct: 419 GTMGYGLPAAIGAQCGNPDSLVIDIAGDASIQMNIQELGTATQYRLPVKVFILNNEWMGM 478

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ Y++R+S+SY D+LPDFVKLAEAYG  G+R+E  S+++  + +A       V 
Sbjct: 479 VRQWQELTYESRFSNSYSDSLPDFVKLAEAYGWKGIRIETESELDAGI-QAMIDHPGPVI 537

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           +D       N +PM+ +G    +M+L  +++
Sbjct: 538 VDCLVHKESNCFPMIPSGASHVDMILYGDNV 568


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: 898
Number of extensions: 46
Number of successful extensions: 5
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: 580
Length adjustment: 36
Effective length of query: 549
Effective length of database: 544
Effective search space:   298656
Effective search space used:   298656
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_059150772.1 V474_RS04395 (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.3051629.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-240  785.5   0.0   1.6e-240  785.3   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059150772.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150772.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  785.3   0.0  1.6e-240  1.6e-240       2     554 ..       6     562 ..       5     565 .. 0.98

  Alignments for each domain:
  == domain 1  score: 785.3 bits;  conditional E-value: 1.6e-240
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +ga+ilvesl ++gve vfGyPGGavlpiydal+ d+ l+hilvrhe +a haa+Gyar++Gk+Gvvl+tsGP
  NCBI__GCF_001046635.1:WP_059150772.1   6 SGANILVESLVRQGVEFVFGYPGGAVLPIYDALFgDERLRHILVRHEAGAGHAAEGYARSTGKPGVVLVTSGP 78 
                                           79********************************9999*********************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Gatn++t+ia+a+lds+Plvv+tGqv+t+liGsd fqe+d +Gi++ +tkh++lvk++++l++++ eaf+ia+
  NCBI__GCF_001046635.1:WP_059150772.1  79 GATNVITAIADAFLDSIPLVVITGQVPTALIGSDGFQEADTVGISRHCTKHNYLVKDPAELAAVIDEAFQIAT 151
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiae..as 217
                                           tGrPGPvl+d+Pkdv+ a+   +   +   + y+p+++g    i++a+e+i++ak Pv + GgGvi a+  a+
  NCBI__GCF_001046635.1:WP_059150772.1 152 TGRPGPVLIDIPKDVQIASAAWNDGPTQRRQRYAPRTQGTAGEIAQAVEMIAAAKAPVFYTGGGVINAGprAT 224
                                           *******************9999998899999**********************************9864488 PP

                             TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap 290
                                           + l+el  ++ +pvt+tl+GlGafp+dh   lgmlGmhGt+eanla+++adl+++vGarfddrvtg l+ fap
  NCBI__GCF_001046635.1:WP_059150772.1 225 QLLRELQAKTGAPVTSTLMGLGAFPADHADWLGMLGMHGTYEANLAMNQADLIVCVGARFDDRVTGRLDAFAP 297
                                           99*********************************************************************** PP

                             TIGR00118 291 eakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke.Wlekieewkkeyilkldeeeesik 362
                                           ++k ihidid ++i+k+v+v++pivGd+  vle++l++  +++ ++   W+++++ w++++ l++  ++++i 
  NCBI__GCF_001046635.1:WP_059150772.1 298 NSKKIHIDIDRSSINKIVRVELPIVGDCAVVLEQMLAEWGSRKGQDLTeWKARVDTWREKKSLSFPLNDDAIM 370
                                           ***************************************9998777666************************ PP

                             TIGR00118 363 Pqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvav 434
                                           Pq  i++l +l+kd + i++t+vGqhqmwaaq++++ +p+k++tsgGlGtmG+GlPaa+Ga+ ++p++ v+++
  NCBI__GCF_001046635.1:WP_059150772.1 371 PQLAIQRLFELTKDkDPIISTEVGQHQMWAAQHFPFFSPNKWLTSGGLGTMGYGLPAAIGAQCGNPDSLVIDI 443
                                           *************9889******************************************************** PP

                             TIGR00118 435 tGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgir 507
                                           +Gd+s+qmn+qel t+++y +pvk+ ilnne++Gmv+qWqel ye r+s+++  s lpdfvklaeayG kgir
  NCBI__GCF_001046635.1:WP_059150772.1 444 AGDASIQMNIQELGTATQYRLPVKVFILNNEWMGMVRQWQELTYESRFSNSYSDS-LPDFVKLAEAYGWKGIR 515
                                           *****************************************************95.***************** PP

                             TIGR00118 508 iekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                           ie+++el++ ++ ++ + +pv++d  v+ke++++Pm+++Ga+  +++
  NCBI__GCF_001046635.1:WP_059150772.1 516 IETESELDAGIQAMIDHPGPVIVDCLVHKESNCFPMIPSGASHVDMI 562
                                           ******************************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (580 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: 17.67
//
[ok]

This GapMind analysis is from Jul 26 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