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_068168649.1 HTA01S_RS07370 acetolactate synthase 3 catalytic subunit

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



>NCBI__GCF_001592305.1:WP_068168649.1
          Length = 591

 Score =  899 bits (2322), Expect = 0.0
 Identities = 439/586 (74%), Positives = 503/586 (85%), Gaps = 4/586 (0%)

Query: 4   AEFSHADSNSSAAP-EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHIL 62
           AE + A + S AAP E+ GAEIL+ AL  EGV+Y+WGYPGGAVL+IYD  +KQ   +H+L
Sbjct: 6   AELASAAAASGAAPQELRGAEILIKALQAEGVKYIWGYPGGAVLHIYDAFYKQDTIQHVL 65

Query: 63  VRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHA 122
           VRHEQAAVHAADGYARATG VGV+LVTSGPG+TNAVTGIATAY+DSIPMV+I G VPT A
Sbjct: 66  VRHEQAAVHAADGYARATGDVGVSLVTSGPGLTNAVTGIATAYMDSIPMVIIAGQVPTAA 125

Query: 123 IGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSR 182
           IG DAFQECDTVGITRPIVKHNFLVKDVRD+A  +KKAF IA +GRPGPVVVDIPKDVS 
Sbjct: 126 IGLDAFQECDTVGITRPIVKHNFLVKDVRDMAMVMKKAFHIARSGRPGPVVVDIPKDVSF 185

Query: 183 NACKYE-YPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQ 241
           N   Y  YP+S+ MRSYNPV KGH GQIRKA+ LL  A+RPYIYTGGGV+L NA  ELR 
Sbjct: 186 NKTAYTGYPESVSMRSYNPVRKGHGGQIRKALQLLLSAKRPYIYTGGGVLLGNAVQELRT 245

Query: 242 LAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVI 301
           L  + G+PVTNTLMGLGA+P T ++F+GMLGMHGT EAN AMQNCDVL+A+GARFDDRVI
Sbjct: 246 LVDMLGYPVTNTLMGLGAYPATDRKFLGMLGMHGTVEANNAMQNCDVLLAVGARFDDRVI 305

Query: 302 GNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREAL 361
           GNP HF    RKIIHIDIDPSSISKRVKVD+PIVG+VKDVL ELI+ ++ S ++P  +AL
Sbjct: 306 GNPKHFAQNERKIIHIDIDPSSISKRVKVDVPIVGDVKDVLTELISMVRESPLRPDEKAL 365

Query: 362 AKWWEQIEQWRSVDCLKYDRSS-EIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQF 419
           A WWE IE WRS DCLKYDR + ++IKPQYVVE +W +TK  DA+I SDVGQHQMWAAQ+
Sbjct: 366 AGWWEAIEGWRSTDCLKYDRGNKDVIKPQYVVETLWNMTKDADAYITSDVGQHQMWAAQY 425

Query: 420 YKFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYD 479
           YKF+EPRRWINSGGLGTMGVG+PYAMGIK A PE EV  +TGEGS+QMCIQELSTCLQY+
Sbjct: 426 YKFNEPRRWINSGGLGTMGVGIPYAMGIKLAKPESEVFCVTGEGSVQMCIQELSTCLQYN 485

Query: 480 TPVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVE 539
           TP+KI +LNN YLGMVRQWQE++Y+ RYSHSYMDALP+FVKLAEAYGHVGM +E+  DVE
Sbjct: 486 TPIKIMALNNRYLGMVRQWQELDYEGRYSHSYMDALPNFVKLAEAYGHVGMLIERPQDVE 545

Query: 540 PALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
            ALREA +LKDRTVF+DF+TDPTENV+PMV+AGKGI+EM LGAEDL
Sbjct: 546 GALREARKLKDRTVFMDFRTDPTENVFPMVRAGKGITEMTLGAEDL 591


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: 1110
Number of extensions: 32
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: 591
Length adjustment: 37
Effective length of query: 548
Effective length of database: 554
Effective search space:   303592
Effective search space used:   303592
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_068168649.1 HTA01S_RS07370 (acetolactate synthase 3 catalytic 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.28462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-253  825.9   0.3   8.9e-253  825.7   0.3    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068168649.1  HTA01S_RS07370 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068168649.1  HTA01S_RS07370 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.7   0.3  8.9e-253  8.9e-253       1     554 [.      22     585 ..      22     588 .. 0.97

  Alignments for each domain:
  == domain 1  score: 825.7 bits;  conditional E-value: 8.9e-253
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaeil+++l++egv++++GyPGGavl+iyda+y ++ ++h+lvrheqaa+haadGyara+G vGv l
  lcl|NCBI__GCF_001592305.1:WP_068168649.1  22 LRGAEILIKALQAEGVKYIWGYPGGAVLHIYDAFYkQDTIQHVLVRHEQAAVHAADGYARATGDVGVSL 90 
                                               68*********************************9999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vtgiatay+ds+P+v+++Gqv+t++iG dafqe+d +Git+p++kh+flvk+++d++ +
  lcl|NCBI__GCF_001592305.1:WP_068168649.1  91 VTSGPGLTNAVTGIATAYMDSIPMVIIAGQVPTAAIGLDAFQECDTVGITRPIVKHNFLVKDVRDMAMV 159
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvl 205
                                               +k+af+ia +GrPGPv+vd+Pkdv+ +++ ++ + e+v++++y+p  kgh  qi+kal+l+ +ak+P +
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 160 MKKAFHIARSGRPGPVVVDIPKDVSFNKTAYTGYpESVSMRSYNPVRKGHGGQIRKALQLLLSAKRPYI 228
                                               ************************98888876544********************************** PP

                                 TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                               + GgGv+ ++a +el+ l+++l  pvt tl+GlGa+p++++++lgmlGmhGt ean a++++d+l+avG
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 229 YTGGGVLLGNAVQELRTLVDMLGYPVTNTLMGLGAYPATDRKFLGMLGMHGTVEANNAMQNCDVLLAVG 297
                                               ********************************************************************* PP

                                 TIGR00118 275 arfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               arfddrv gn ++fa++  kiihididP++i+k vkvd+pivGd+k vl+el++ ++e     ++k   
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 298 ARFDDRVIGNPKHFAQNErKIIHIDIDPSSISKRVKVDVPIVGDVKDVLTELISMVRESplrpDEKALA 366
                                               ***************87527*************************************998876444445 PP

                                 TIGR00118 339 .Wlekieewkkeyilkldeeees.ikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404
                                                W+e ie w+++ +lk+d+ ++  ikPq+v+++l++++kd +a++t+dvGqhqmwaaq+yk+++pr++i
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 367 gWWEAIEGWRSTDCLKYDRGNKDvIKPQYVVETLWNMTKDaDAYITSDVGQHQMWAAQYYKFNEPRRWI 435
                                               7***************99866554***************999*************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +sgGlGtmG G+P a+G+k+akpe++v +vtG+gs+qm +qelst+ +y++p+ki+ lnn++lGmv+qW
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 436 NSGGLGTMGVGIPYAMGIKLAKPESEVFCVTGEGSVQMCIQELSTCLQYNTPIKIMALNNRYLGMVRQW 504
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541
                                               qel ye+rys++++ + lp+fvklaeayG++g+ ie+p+++e +l+ea + k + v++d++ d +e+v+
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 505 QELDYEGRYSHSYMDA-LPNFVKLAEAYGHVGMLIERPQDVEGALREARKLKdRTVFMDFRTDPTENVF 572
                                               ***************5.*******************************9987699************** PP

                                 TIGR00118 542 PmvapGagldelv 554
                                               Pmv  G+g++e+ 
  lcl|NCBI__GCF_001592305.1:WP_068168649.1 573 PMVRAGKGITEMT 585
                                               ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (591 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.08
//
[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