Alignments for a candidate for ilvI in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Hydrogenophaga taeniospiralis NBRC 102512

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_068171493.1 HTA01S_RS12055 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_001592305.1:WP_068171493.1
          Length = 607

 Score =  515 bits (1327), Expect = e-150
 Identities = 271/566 (47%), Positives = 371/566 (65%), Gaps = 11/566 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GAE+L+  L   G++ V+GYPGGA L +YD L K+    H+LVRHEQAAVHAA+GYAR T
Sbjct: 35  GAELLLDTLLACGIDTVFGYPGGAALPLYDALFKRPALRHVLVRHEQAAVHAAEGYARCT 94

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           G+VGV LVTSGPGV+N +TG+  A+ D+IP++ I+G V T  IG  AFQECD +G++RP+
Sbjct: 95  GRVGVVLVTSGPGVSNTLTGLLDAHSDAIPVLCISGQVATGVIGTQAFQECDAIGMSRPV 154

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRN--ACKYEYPKSIDMRSY 198
            K N  ++D  ++ A ++KA  IAA+G+PGPV++D+PKDV     A         +  + 
Sbjct: 155 TKWNHQLRDASEVVAVVRKALRIAASGKPGPVLLDVPKDVQLQCPATPAGEDGGDEFTAL 214

Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLMG 256
            P+    +  +R+A  L+  A +P +Y GGG++ A   A +   +LA     P T TLMG
Sbjct: 215 PPLPT--AAALRRAAGLILEARQPVLYGGGGLISAGPAACEAFTRLARWLHLPTTLTLMG 272

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGAFP +  +F+GMLGMHGT EAN AM + D+++ +GARFDDRV    + F  +ARK IH
Sbjct: 273 LGAFPASDPRFLGMLGMHGTLEANQAMHHADLIVCVGARFDDRVTSKLSDFAPRARK-IH 331

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           +DID S+I+K V VD+ + G+   VLQ L+A + A    P  + L  WW++IE WR    
Sbjct: 332 LDIDASNINKVVPVDVALQGDCGAVLQALLASLPAE--PPSAQRLDAWWQRIEGWRGFHS 389

Query: 377 LKYDRSSEIIKPQYVVEKIW-ELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           L +   S+ I PQ ++ ++  +L   DA + +DVGQHQMWAAQ  +F+ PRRW+ SGG G
Sbjct: 390 LGFTPRSDAILPQQLMHELQRQLAPRDAIVATDVGQHQMWAAQHLRFEAPRRWLTSGGAG 449

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP A+G + A P+K VV ++G+ SI M IQELST +Q+ TPVK+   NNGY+GMV
Sbjct: 450 TMGYGLPAAIGAQIAHPDKTVVCVSGDASILMNIQELSTAVQHGTPVKVVLSNNGYMGMV 509

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ + NR SHS+  ALPDFV LA A+G    RV    ++  AL E         FL
Sbjct: 510 RQWQELVHGNRISHSWNAALPDFVALARAFGWGARRVGAPDELADALAECL-AHAGPFFL 568

Query: 556 DFQTDPTENVWPMVQAGKGISEMLLG 581
           D +  P EN +PM+ AG+G  EM+LG
Sbjct: 569 DVRVVPQENCYPMIPAGRGHQEMMLG 594


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: 921
Number of extensions: 37
Number of successful extensions: 7
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: 607
Length adjustment: 37
Effective length of query: 548
Effective length of database: 570
Effective search space:   312360
Effective search space used:   312360
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_068171493.1 HTA01S_RS12055 (acetolactate synthase, large subunit, biosynthetic type)
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.15921.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-214  699.2   0.0   2.2e-214  698.9   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068171493.1  HTA01S_RS12055 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068171493.1  HTA01S_RS12055 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  698.9   0.0  2.2e-214  2.2e-214       2     554 ..      34     592 ..      33     595 .. 0.96

  Alignments for each domain:
  == domain 1  score: 698.9 bits;  conditional E-value: 2.2e-214
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +gae+l+++l + g++tvfGyPGGa lp+ydal+    l+h+lvrheqaa+haa+Gyar++G+vGvvl+
  lcl|NCBI__GCF_001592305.1:WP_068171493.1  34 NGAELLLDTLLACGIDTVFGYPGGAALPLYDALFkRPALRHVLVRHEQAAVHAAEGYARCTGRVGVVLV 102
                                               69********************************8889******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG  n++tg+++a+ d++P++ ++Gqvat +iG+ afqe+d +G+++pvtk+++++++a+++ +++
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 103 TSGPGVSNTLTGLLDAHSDAIPVLCISGQVATGVIGTQAFQECDAIGMSRPVTKWNHQLRDASEVVAVV 171
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               ++a+ ia++G+PGPvl+d+Pkdv+ +   ++  e+      ++   +  + +++a+ li +a++Pvl+ 
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 172 RKALRIAASGKPGPVLLDVPKDVQLQCPATPAGEDGGDEFTALPPLPTAAALRRAAGLILEARQPVLYG 240
                                               ************************999999988776666666666788899****************** PP

                                 TIGR00118 208 GgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               GgG+i a+  a e +++la  l++p t tl+GlGafp+ +p++lgmlGmhGt ean a+++adl+++vG
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 241 GGGLISAGpaACEAFTRLARWLHLPTTLTLMGLGAFPASDPRFLGMLGMHGTLEANQAMHHADLIVCVG 309
                                               *****886447799******************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wl 340
                                               arfddrvt++l+ fap+a+ ih+did ++i+k+v vd+++ Gd+  vl+ ll+ l +e  + +  + W+
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 310 ARFDDRVTSKLSDFAPRARKIHLDIDASNINKVVPVDVALQGDCGAVLQALLASLPAEppSAQRLDaWW 378
                                               *******************************************************999664444446** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskl.lkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               ++ie w+  + l +  ++++i Pq++++el+++ ++ +aiv+tdvGqhqmwaaq++++++pr+++tsgG
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 379 QRIEGWRGFHSLGFTPRSDAILPQQLMHELQRQlAPRDAIVATDVGQHQMWAAQHLRFEAPRRWLTSGG 447
                                               ******************************9761567******************************** PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               +GtmG+GlPaa+Ga++a+p++tvv+v+Gd+s+ mn+qelst+v+ ++pvk+v+ nn ++Gmv+qWqel+
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 448 AGTMGYGLPAAIGAQIAHPDKTVVCVSGDASILMNIQELSTAVQHGTPVKVVLSNNGYMGMVRQWQELV 516
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546
                                               + +r s++  a  lpdfv+la+a+G  + r+  p+el+++l+e l++ +p +ldv+v  +e+++Pm++ 
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 517 HGNRISHSWNA-ALPDFVALARAFGWGARRVGAPDELADALAECLAHAGPFFLDVRVVPQENCYPMIPA 584
                                               ********999.5******************************************************** PP

                                 TIGR00118 547 Gagldelv 554
                                               G g +e++
  lcl|NCBI__GCF_001592305.1:WP_068171493.1 585 GRGHQEMM 592
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (607 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: 00:00:00.03
# Mc/sec: 11.13
//
[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