Alignments for a candidate for ilvI in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pyrolobus fumarii 1A

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_014027226.1 PYRFU_RS08320 acetolactate synthase, large subunit, biosynthetic type

Query= curated2:P37251
         (574 letters)



>NCBI__GCF_000223395.1:WP_014027226.1
          Length = 571

 Score =  408 bits (1048), Expect = e-118
 Identities = 223/551 (40%), Positives = 328/551 (59%), Gaps = 14/551 (2%)

Query: 26  ESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHI-LPRHEQGAIHAAEGYARVSGKPGVV 84
           ++L++     +FG  GG+++  YD +   G  +I + RHEQGA HAA+ Y RV  +P +V
Sbjct: 7   KTLREMGATDVFGVTGGSIMAFYDAMEVVGGFNIYMFRHEQGAAHAADAYGRVKKRPAIV 66

Query: 85  IATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITMPVTKHSYQ 144
             TSGPGATN+VTG+A+A +DS P +  TGQV T+V G DAFQE D++G+  P+TK  YQ
Sbjct: 67  AVTSGPGATNIVTGVANAYMDSSPALFITGQVPTTVFGRDAFQETDMVGVVAPITKFVYQ 126

Query: 145 VRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQP--TTEP 202
           +R+PE+    IK A+ +A  GRPGP L+D P+DV     + + D  + L  Y+     +P
Sbjct: 127 IRRPEEAVPAIKTAYKLAIMGRPGPTLVDFPRDVQLRRCDCTSDGLLPL-NYEKFKAPDP 185

Query: 203 NYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLGGFPADH 262
           +   I +    + SA++PVIL G GV    A  E+   AE+   P+  TL G    PADH
Sbjct: 186 DPRLIEEAARLLLSARRPVILVGGGVYWSGAWPEVIEIAERLWAPIVTTLTGKNSVPADH 245

Query: 263 PLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTGNLKHFARNAKIAHIDIDPAEIG 322
           PL +G AGMHG   A+ AL   D+++++G RF DR  G  +   +  KI HIDIDP+EIG
Sbjct: 246 PLVMGPAGMHGRAEADAALANADVILAVGTRFSDRTVGRFEPELKEKKIIHIDIDPSEIG 305

Query: 323 KIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLAEWKEEYPLWYVDNEEE------ 376
           K +K  + +V D+K  L+ LI+   K  + +    +  +W       Y D  E+      
Sbjct: 306 KNVKPAVGIVADAKKALRMLIE---KLPEVARRDTKFVDWLLYIRRRYEDAMEKLAERMK 362

Query: 377 GFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPAA 436
            F P K+++ + +    + I AT VG HQMWS   +       W+TS GLGTMGF +PAA
Sbjct: 363 PFAPWKVLKLLRRIVPRDTITATGVGSHQMWSEIHWDVYIPGTWLTSAGLGTMGFCVPAA 422

Query: 437 IGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFYE 496
           IGA++A  + TV+ + GDG FQMT+  L ++R+ NLP   VI +N  L +V+QWQ   YE
Sbjct: 423 IGAKIAAPERTVLCIDGDGSFQMTMNNLALVRDYNLPAIFVIFDNRALMLVKQWQIFLYE 482

Query: 497 ERYSESKFASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVIDVRVASE-EK 555
            R   + F  +PDFVK++EAY I+G+R +   E ++ +  A+ + EP+V+D+ +  E + 
Sbjct: 483 RRIVATHFTERPDFVKVAEAYDIEGVRPADYQELEKWVRWAVRNNEPLVVDIMIDREMDI 542

Query: 556 VFPMVAPGKGL 566
           V+P V PG+ L
Sbjct: 543 VYPWVKPGEWL 553


Lambda     K      H
   0.317    0.135    0.391 

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: 833
Number of extensions: 37
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: 574
Length of database: 571
Length adjustment: 36
Effective length of query: 538
Effective length of database: 535
Effective search space:   287830
Effective search space used:   287830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_014027226.1 PYRFU_RS08320 (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.21104.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-182  591.5   0.0   9.9e-182  591.1   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_014027226.1  PYRFU_RS08320 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014027226.1  PYRFU_RS08320 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.1   0.0  9.9e-182  9.9e-182       7     552 ..       5     555 ..       2     559 .. 0.96

  Alignments for each domain:
  == domain 1  score: 591.1 bits;  conditional E-value: 9.9e-182
                                 TIGR00118   7 lveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                               + ++l++ g   vfG  GG+++ +yda+   ++++  + rheq+aahaad y r+  ++ +v +tsGPG
  lcl|NCBI__GCF_000223395.1:WP_014027226.1   5 VAKTLREMGATDVFGVTGGSIMAFYDAMEvVGGFNIYMFRHEQGAAHAADAYGRVKKRPAIVAVTSGPG 73 
                                               77999***********************999************************************** PP

                                 TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafe 143
                                               atn+vtg+a+ay+ds+P + +tGqv+t++ G dafqe d++G+  p+tk+ ++++++e+    +k a++
  lcl|NCBI__GCF_000223395.1:WP_014027226.1  74 ATNIVTGVANAYMDSSPALFITGQVPTTVFGRDAFQETDMVGVVAPITKFVYQIRRPEEAVPAIKTAYK 142
                                               ********************************************************************* PP

                                 TIGR00118 144 iastGrPGPvlvdlPkdvteaeieleveekvelpgykptv.kghklqikkaleliekakkPvllvGgGv 211
                                               +a  GrPGP lvd+P+dv+ + ++ + +  + l   k +   ++++ i++a+ l+ +a++Pv+lvGgGv
  lcl|NCBI__GCF_000223395.1:WP_014027226.1 143 LAIMGRPGPTLVDFPRDVQLRRCDCTSDGLLPLNYEKFKApDPDPRLIEEAARLLLSARRPVILVGGGV 211
                                               ****************************9999987777653678999********************** PP

                                 TIGR00118 212 iiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddr 280
                                                 ++a  e+ e+aerl +p++ttl G+ ++p+dhpl +g +GmhG++ea+ a+ +ad+++avG+rf+dr
  lcl|NCBI__GCF_000223395.1:WP_014027226.1 212 YWSGAWPEVIEIAERLWAPIVTTLTGKNSVPADHPLVMGPAGMHGRAEADAALANADVILAVGTRFSDR 280
                                               ********************************************************************* PP

                                 TIGR00118 281 vtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke...Wlekieew 346
                                               + g  +   +e kiihididP+eigknvk ++ iv dakk l+ l++kl e+ +++++   Wl  i++ 
  lcl|NCBI__GCF_000223395.1:WP_014027226.1 281 TVGRFEPELKEKKIIHIDIDPSEIGKNVKPAVGIVADAKKALRMLIEKLPEVARRDTKfvdWLLYIRRR 349
                                               ****************************************************88887744577777777 PP

                                 TIGR00118 347 kkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfG 415
                                                ++ + kl e+ ++++P kv+k l ++++ ++i +t+vG hqmw+  ++++  p +++ts+GlGtmGf 
  lcl|NCBI__GCF_000223395.1:WP_014027226.1 350 YEDAMEKLAERMKPFAPWKVLKLLRRIVPRDTITATGVGSHQMWSEIHWDVYIPGTWLTSAGLGTMGFC 418
                                               777777788888889999*************************************************** PP

                                 TIGR00118 416 lPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryse 484
                                               +Paa+Gak+a pe tv++++Gdgsfqm++++l+ +++y++p + vi++n+ l +vkqWq ++ye+r  +
  lcl|NCBI__GCF_000223395.1:WP_014027226.1 419 VPAAIGAKIAAPERTVLCIDGDGSFQMTMNNLALVRDYNLPAIFVIFDNRALMLVKQWQIFLYERRIVA 487
                                               ********************************************************************* PP

                                 TIGR00118 485 tklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeee.vlPmvapGaglde 552
                                               t+++ e pdfvk+aeay ++g+r ++ +ele+ ++ a++++ep+++d+ +d+e + v+P v pG  l++
  lcl|NCBI__GCF_000223395.1:WP_014027226.1 488 THFT-ERPDFVKVAEAYDIEGVRPADYQELEKWVRWAVRNNEPLVVDIMIDREMDiVYPWVKPGEWLTN 555
                                               ****.7*********************************************986538*******98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (571 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: 00:00:00.03
# Mc/sec: 9.75
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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