GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Leptospirillum ferrooxidans C2-3

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_014450635.1 LFE_RS12760 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_000284315.1:WP_014450635.1
          Length = 583

 Score =  627 bits (1616), Expect = 0.0
 Identities = 312/571 (54%), Positives = 404/571 (70%), Gaps = 7/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GAE+L+ +L  E V++++GYPGG VL I+D L K    + +L RHEQ AVHAA+GYA
Sbjct: 2   KMSGAEMLLESLKRENVQHIFGYPGGVVLPIFDALFKDPSLQVVLTRHEQGAVHAAEGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+T KVGV LVTSGPG TN VTG+A A +DSIP+VVITG VPT  IG DAFQE D VGI+
Sbjct: 62  RSTNKVGVVLVTSGPGATNTVTGLADANMDSIPIVVITGQVPTKMIGNDAFQEADIVGIS 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHNFLV+ ++DL   IK+AF+IA TGRPGPV+VD+PKDV  +   + YP S+ +RS
Sbjct: 122 RSCTKHNFLVRKIQDLPRIIKEAFYIARTGRPGPVLVDLPKDVIVDRADFIYPDSVSIRS 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  +G+  QIRKA   +  A+RP +Y GGG++ ++A+ EL  L  LT  P T TLMGL
Sbjct: 182 YNPTMQGNRWQIRKAAQAISKAKRPVLYAGGGIISSDATKELLDLVTLTNIPTTLTLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GA  GT  +F+GMLGMHGTY ANMA+ +CD+LIA+G RFDDRV G  + F+  + K+IHI
Sbjct: 242 GALSGTHPRFMGMLGMHGTYAANMAIHHCDLLIAVGVRFDDRVTGKISEFSPHS-KVIHI 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKP----KREALAKWWEQIEQWRS 373
           DIDP+SI K   VDIPIVG+ K +L++LI +IK  + KP    K + +  W EQ+E+W  
Sbjct: 301 DIDPTSIRKNFHVDIPIVGDAKHILKDLIEEIKELN-KPEPPSKEKLIDPWIEQVEEWEK 359

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
              L Y+  +E+IKPQYV+EK+++ T+GD  + +DVGQHQMW AQF+KF +P  W+ SGG
Sbjct: 360 EHPLTYEHDTEVIKPQYVIEKVYQFTQGDCIVSTDVGQHQMWTAQFFKFIKPNTWLTSGG 419

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG G P A+G +KA P+K V+ ITGEGS  M IQEL+T    D PVKI  LNN YLG
Sbjct: 420 LGTMGYGFPAAIGAQKAHPDKRVIAITGEGSFMMNIQELATVASLDIPVKIVILNNKYLG 479

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQE  Y  RYS S++   PDFVKLAEA+G VG++  +  +VE  + + F  +   V
Sbjct: 480 MVRQWQEFFYGGRYSSSFIGQSPDFVKLAEAFGIVGLKASRHDEVENIILDGFSRRG-PV 538

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584
            ++F  DP ENV+PMV AG    EM+  A +
Sbjct: 539 LMEFHVDPEENVFPMVPAGGSNIEMIFEAPE 569


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: 918
Number of extensions: 36
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: 583
Length adjustment: 36
Effective length of query: 549
Effective length of database: 547
Effective search space:   300303
Effective search space used:   300303
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_014450635.1 LFE_RS12760 (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.1059616.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-261  854.4   0.2   2.1e-261  854.2   0.2    1.0  1  NCBI__GCF_000284315.1:WP_014450635.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014450635.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  854.2   0.2  2.1e-261  2.1e-261       1     554 [.       3     564 ..       3     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 854.2 bits;  conditional E-value: 2.1e-261
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           ++gae+l+eslk+e+v+++fGyPGG vlpi+dal+ d  l+ +l+rheq+a+haa+Gyar++ kvGvvl+tsG
  NCBI__GCF_000284315.1:WP_014450635.1   3 MSGAEMLLESLKRENVQHIFGYPGGVVLPIFDALFkDPSLQVVLTRHEQGAVHAAEGYARSTNKVGVVLVTSG 75 
                                           79*********************************8889********************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vtg+a+a +ds+P+vv+tGqv+t++iG+dafqe+di+Gi++++tkh+flv+k +dlp+i+keaf+ia
  NCBI__GCF_000284315.1:WP_014450635.1  76 PGATNTVTGLADANMDSIPIVVITGQVPTKMIGNDAFQEADIVGISRSCTKHNFLVRKIQDLPRIIKEAFYIA 148
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218
                                            tGrPGPvlvdlPkdv     ++ ++++v++++y+pt++g++ qi+ka+++i+kak+Pvl++GgG+i ++a++
  NCBI__GCF_000284315.1:WP_014450635.1 149 RTGRPGPVLVDLPKDVIVDRADFIYPDSVSIRSYNPTMQGNRWQIRKAAQAISKAKRPVLYAGGGIISSDATK 221
                                           ************************************************************************* PP

                             TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291
                                           el +l+  ++ip t tl+GlGa+  +hp+++gmlGmhGt++an+a++++dlliavG+rfddrvtg++++f+p+
  NCBI__GCF_000284315.1:WP_014450635.1 222 ELLDLVTLTNIPTTLTLMGLGALSGTHPRFMGMLGMHGTYAANMAIHHCDLLIAVGVRFDDRVTGKISEFSPH 294
                                           ************************************************************************* PP

                             TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee.......ekkeke.Wlekieewkkeyilklde 356
                                           +k+ihididP++i kn +vdipivGdak++l++l++++ke        ++k ++ W+e++eew ke++l++++
  NCBI__GCF_000284315.1:WP_014450635.1 295 SKVIHIDIDPTSIRKNFHVDIPIVGDAKHILKDLIEEIKELnkpeppsKEKLIDpWIEQVEEWEKEHPLTYEH 367
                                           **************************************99888888643444458****************** PP

                             TIGR00118 357 eeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429
                                           + e ikPq+vi++++++++++ iv+tdvGqhqmw+aqf+k+ kp++++tsgGlGtmG+G+Paa+Ga+ a+p++
  NCBI__GCF_000284315.1:WP_014450635.1 368 DTEVIKPQYVIEKVYQFTQGDCIVSTDVGQHQMWTAQFFKFIKPNTWLTSGGLGTMGYGFPAAIGAQKAHPDK 440
                                           ************************************************************************* PP

                             TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                            v+a+tG+gsf+mn+qel+t++ +dipvkivilnn++lGmv+qWqe+fy +rys++ +++ +pdfvklaea+G
  NCBI__GCF_000284315.1:WP_014450635.1 441 RVIAITGEGSFMMNIQELATVASLDIPVKIVILNNKYLGMVRQWQEFFYGGRYSSSFIGQ-SPDFVKLAEAFG 512
                                           ***********************************************************6.************ PP

                             TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                           ++g++ ++++e+e+ + + ++ ++pvl++++vd ee+v+Pmv+ G+++ e++
  NCBI__GCF_000284315.1:WP_014450635.1 513 IVGLKASRHDEVENIILDGFSRRGPVLMEFHVDPEENVFPMVPAGGSNIEMI 564
                                           ************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (583 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: 20.99
//
[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