Alignments for a candidate for ilvI in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Polaromonas naphthalenivorans CJ2

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011801116.1 PNAP_RS08580 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000015505.1:WP_011801116.1
          Length = 592

 Score =  893 bits (2307), Expect = 0.0
 Identities = 437/580 (75%), Positives = 497/580 (85%), Gaps = 3/580 (0%)

Query: 9   ADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQA 68
           A S  +   ++ GAEILV AL  EGV+Y+WGYPGGAVL+IYD  +KQ   +H+LVRHEQA
Sbjct: 13  ATSAQTNPQDLRGAEILVKALQAEGVKYIWGYPGGAVLHIYDAFYKQDSIQHVLVRHEQA 72

Query: 69  AVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAF 128
           AVHAADGYARATG VGVALVTSGPG+TNAVTGIATAY+DSIPMV+I+G VPT AIG DAF
Sbjct: 73  AVHAADGYARATGDVGVALVTSGPGLTNAVTGIATAYMDSIPMVIISGQVPTAAIGLDAF 132

Query: 129 QECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYE 188
           QECDTVGITRPIVKHNFLVKDVRD+A T+KKAF IA TGRPGPVVVD+PKDVS N   Y 
Sbjct: 133 QECDTVGITRPIVKHNFLVKDVRDMAETMKKAFHIARTGRPGPVVVDVPKDVSFNKTLYT 192

Query: 189 -YPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTG 247
            YPKS++MRSYNPV KGH+GQIRKA+ LL  A+RPYIYTGGGV+L+NAS ELR L  + G
Sbjct: 193 GYPKSVEMRSYNPVRKGHAGQIRKALHLLMAAKRPYIYTGGGVLLSNASQELRTLVDMLG 252

Query: 248 HPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHF 307
           +P T+TLMGLGA+P + K+F+GMLGMHGT EAN AMQNCDVL+A+GARFDDRVIGNP HF
Sbjct: 253 YPCTHTLMGLGAYPASDKKFLGMLGMHGTLEANNAMQNCDVLLAVGARFDDRVIGNPKHF 312

Query: 308 TSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQ 367
               RKIIHIDIDPSSISKRVKVDIPIVG+VKDVL ELIA I+ S +KP  +AL  WW  
Sbjct: 313 AQNERKIIHIDIDPSSISKRVKVDIPIVGDVKDVLTELIAMIRESGLKPDADALGGWWST 372

Query: 368 IEQWRSVDCLKYDRSS-EIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQFYKFDEP 425
           I++WR  DC+KY   + ++IKPQYVVE +W +TK  D +I SDVGQHQMWAAQ+YKFDEP
Sbjct: 373 IDEWRKRDCMKYSLGTGDVIKPQYVVETLWNMTKDADTYITSDVGQHQMWAAQYYKFDEP 432

Query: 426 RRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKIC 485
           RRWINSGGLGTMGVG+PYAMGIK A P+ EV  ITGEGS+QMCIQELSTCLQY+TP+KI 
Sbjct: 433 RRWINSGGLGTMGVGIPYAMGIKLAKPDSEVFCITGEGSVQMCIQELSTCLQYNTPIKIV 492

Query: 486 SLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREA 545
           SLNN YLGMVRQWQEIEY  RYS SYMDALP+FVKLAEAYGHVGM +EK  DVEPALREA
Sbjct: 493 SLNNRYLGMVRQWQEIEYAGRYSSSYMDALPNFVKLAEAYGHVGMLIEKPQDVEPALREA 552

Query: 546 FRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
            +LKDRTVF+DF+TDPTENV+PMV+AGKGI+EMLLG+EDL
Sbjct: 553 RKLKDRTVFMDFRTDPTENVFPMVKAGKGITEMLLGSEDL 592


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: 1116
Number of extensions: 31
Number of successful extensions: 4
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: 592
Length adjustment: 37
Effective length of query: 548
Effective length of database: 555
Effective search space:   304140
Effective search space used:   304140
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_011801116.1 PNAP_RS08580 (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.2378.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-253  827.5   0.2   2.9e-253  827.3   0.2    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011801116.1  PNAP_RS08580 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011801116.1  PNAP_RS08580 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  827.3   0.2  2.9e-253  2.9e-253       1     554 [.      23     586 ..      23     589 .. 0.96

  Alignments for each domain:
  == domain 1  score: 827.3 bits;  conditional E-value: 2.9e-253
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaeilv++l++egv++++GyPGGavl+iyda+y ++ ++h+lvrheqaa+haadGyara+G vGv+l
  lcl|NCBI__GCF_000015505.1:WP_011801116.1  23 LRGAEILVKALQAEGVKYIWGYPGGAVLHIYDAFYkQDSIQHVLVRHEQAAVHAADGYARATGDVGVAL 91 
                                               68*********************************9999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vtgiatay+ds+P+v+++Gqv+t++iG dafqe+d +Git+p++kh+flvk+++d++e+
  lcl|NCBI__GCF_000015505.1:WP_011801116.1  92 VTSGPGLTNAVTGIATAYMDSIPMVIISGQVPTAAIGLDAFQECDTVGITRPIVKHNFLVKDVRDMAET 160
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeiel.eveekvelpgykptvkghklqikkaleliekakkPvl 205
                                               +k+af+ia tGrPGPv+vd+Pkdv+ +++ +  ++++ve+++y+p  kgh  qi+kal+l+++ak+P +
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 161 MKKAFHIARTGRPGPVVVDVPKDVSFNKTLYtGYPKSVEMRSYNPVRKGHAGQIRKALHLLMAAKRPYI 229
                                               ************************97666551677********************************** PP

                                 TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               + GgGv+ ++as+el+ l+++l  p t+tl+GlGa+p+ ++++lgmlGmhGt ean a++++d+l+avG
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 230 YTGGGVLLSNASQELRTLVDMLGYPCTHTLMGLGAYPASDKKFLGMLGMHGTLEANNAMQNCDVLLAVG 298
                                               ********************************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               arfddrv gn ++fa++  kiihididP++i+k vkvdipivGd+k vl+el++ ++e     + +   
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 299 ARFDDRVIGNPKHFAQNErKIIHIDIDPSSISKRVKVDIPIVGDVKDVLTELIAMIRESglkpDADALG 367
                                               ***************87527*************************************998874344444 PP

                                 TIGR00118 339 .Wlekieewkkeyilklde.eeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404
                                                W++ i+ew+k+ ++k++  + + ikPq+v+++l++++kd ++++t+dvGqhqmwaaq+yk+++pr++i
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 368 gWWSTIDEWRKRDCMKYSLgTGDVIKPQYVVETLWNMTKDaDTYITSDVGQHQMWAAQYYKFDEPRRWI 436
                                               8***************88715566***************999*************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +sgGlGtmG G+P a+G+k+akp+++v ++tG+gs+qm +qelst+ +y++p+kiv lnn++lGmv+qW
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 437 NSGGLGTMGVGIPYAMGIKLAKPDSEVFCITGEGSVQMCIQELSTCLQYNTPIKIVSLNNRYLGMVRQW 505
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541
                                               qe+ y +rys++++ + lp+fvklaeayG++g+ iekp+++e +l+ea + k + v++d++ d +e+v+
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 506 QEIEYAGRYSSSYMDA-LPNFVKLAEAYGHVGMLIEKPQDVEPALREARKLKdRTVFMDFRTDPTENVF 573
                                               ***************5.*******************************9987699************** PP

                                 TIGR00118 542 PmvapGagldelv 554
                                               Pmv  G+g++e++
  lcl|NCBI__GCF_000015505.1:WP_011801116.1 574 PMVKAGKGITEML 586
                                               ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (592 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.51
//
[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