Alignments for a candidate for ilvI in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Ammonifex degensii KC4

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_015738271.1 ADEG_RS01130 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000024605.1:WP_015738271.1
          Length = 552

 Score =  583 bits (1504), Expect = e-171
 Identities = 307/561 (54%), Positives = 386/561 (68%), Gaps = 12/561 (2%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78
           + G EIL+  L EEGVE V+GYPGGAVL IYD L+ + +  HIL RHEQAA HAADGYAR
Sbjct: 3   LTGGEILLKCLQEEGVEVVFGYPGGAVLPIYDALY-EGEIRHILTRHEQAAAHAADGYAR 61

Query: 79  ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138
           ATG+ GV L TSGPG TN VTGIATAY+DS P+V  TG VPT  IG+DAFQE D  GIT 
Sbjct: 62  ATGRPGVCLATSGPGATNLVTGIATAYMDSSPVVAFTGQVPTSLIGRDAFQEADITGITM 121

Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198
           PI KHNFLVKDV+DLA  +K AF IA TGRPGPV+VDIP+DVS    +YE    + +  Y
Sbjct: 122 PITKHNFLVKDVKDLARVVKAAFHIATTGRPGPVLVDIPRDVSGAETEYEPVTEVRLPGY 181

Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLG 258
            PV      QI+KA  L+  +ERP I  GGGV+ + A++EL +LA L   PV  TLMG+G
Sbjct: 182 RPVYDPDPEQIKKAAKLIATSERPVIIAGGGVIQSGATEELVRLAELIMAPVATTLMGIG 241

Query: 259 AFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHID 318
            FPG     +GMLGMHGT  AN A+   D+LIA+G R DDR+ G    F  +A K+IHID
Sbjct: 242 GFPGNHPLSLGMLGMHGTRYANYAVSESDLLIAVGTRLDDRITGKIESFAPEA-KVIHID 300

Query: 319 IDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLK 378
           IDP+ + K V+VD+PIVG++K  L+ LI  +       ++     W E+IE W+    L 
Sbjct: 301 IDPAELGKNVRVDVPIVGDLKRALKALIEFL-------EKTPHPAWLEKIETWKREYPLT 353

Query: 379 YDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMG 438
           ++ +   +KPQ++V +IWE+TKG+A I ++VGQ+QMWAAQFY F  PR +I SGGLGTMG
Sbjct: 354 FEENGR-LKPQFIVRQIWEVTKGEARIATEVGQNQMWAAQFYTFTRPRSFITSGGLGTMG 412

Query: 439 VGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQW 498
            G P A+G++ A PE+ V  I G+GSIQM IQEL+T + YD PV +  LNNG+LGMVRQW
Sbjct: 413 FGFPAAIGVQVACPEEVVFDIAGDGSIQMNIQELATAVSYDLPVNVAILNNGFLGMVRQW 472

Query: 499 QEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQ 558
           QE+ Y  RYS++ +   PDFVK+AEAYG  G+RV K  +V PAL +A     + VFLDF 
Sbjct: 473 QELFYRRRYSYTEL-YNPDFVKVAEAYGAEGIRVTKPEEVRPALEQAI-ASPKPVFLDFI 530

Query: 559 TDPTENVWPMVQAGKGISEML 579
            +  ENV PMV  G+ I +ML
Sbjct: 531 IEREENVMPMVPPGESIGKML 551


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: 919
Number of extensions: 43
Number of successful extensions: 6
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: 552
Length adjustment: 36
Effective length of query: 549
Effective length of database: 516
Effective search space:   283284
Effective search space used:   283284
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_015738271.1 ADEG_RS01130 (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.2900.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-268  876.2   0.0   5.2e-268  876.0   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015738271.1  ADEG_RS01130 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738271.1  ADEG_RS01130 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.0   0.0  5.2e-268  5.2e-268       1     554 [.       3     551 ..       3     552 .] 0.99

  Alignments for each domain:
  == domain 1  score: 876.0 bits;  conditional E-value: 5.2e-268
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+g+eil++ l++egve+vfGyPGGavlpiydaly++e++hil+rheqaaahaadGyara+G++Gv+la
  lcl|NCBI__GCF_000024605.1:WP_015738271.1   3 LTGGEILLKCLQEEGVEVVFGYPGGAVLPIYDALYEGEIRHILTRHEQAAAHAADGYARATGRPGVCLA 71 
                                               689****************************************************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgiatay+ds+P+v++tGqv+tsliG dafqe+di+Git+p+tkh+flvk+++dl++++
  lcl|NCBI__GCF_000024605.1:WP_015738271.1  72 TSGPGATNLVTGIATAYMDSSPVVAFTGQVPTSLIGRDAFQEADITGITMPITKHNFLVKDVKDLARVV 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k+af+ia+tGrPGPvlvd+P+dv+ ae+e+e  ++v lpgy+p   +++ qikka++li+++++Pv+++
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 141 KAAFHIATTGRPGPVLVDIPRDVSGAETEYEPVTEVRLPGYRPVYDPDPEQIKKAAKLIATSERPVIIA 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi+++a+eel++lae + +pv+ttl+G+G+fp +hpl+lgmlGmhGt++an+avse+dlliavG+r
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 210 GGGVIQSGATEELVRLAELIMAPVATTLMGIGGFPGNHPLSLGMLGMHGTRYANYAVSESDLLIAVGTR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               +ddr+tg++++fapeak+ihididPae+gknv+vd+pivGd k+ l+ l++ l+++ +    Wlekie 
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 279 LDDRITGKIESFAPEAKVIHIDIDPAELGKNVRVDVPIVGDLKRALKALIEFLEKTPHPA--WLEKIET 345
                                               *****************************************************9998877..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               wk+ey+l+++e ++ +kPq +++++++++k+ea ++t+vGq+qmwaaqfy++++pr+fitsgGlGtmGf
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 346 WKREYPLTFEE-NGRLKPQFIVRQIWEVTKGEARIATEVGQNQMWAAQFYTFTRPRSFITSGGLGTMGF 413
                                               ******99875.678****************************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+Paa+G++va pee v +++Gdgs+qmn+qel+t+v yd+pv + ilnn +lGmv+qWqelfy++rys
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 414 GFPAAIGVQVACPEEVVFDIAGDGSIQMNIQELATAVSYDLPVNVAILNNGFLGMVRQWQELFYRRRYS 482
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                                t+l +  pdfvk+aeayG++gir++kpee+  +l++a++s +pv+ld+ +++ee+v+Pmv+pG ++ +
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 483 YTELYN--PDFVKVAEAYGAEGIRVTKPEEVRPALEQAIASPKPVFLDFIIEREENVMPMVPPGESIGK 549
                                               *****7..*********************************************************9998 PP

                                 TIGR00118 553 lv 554
                                               ++
  lcl|NCBI__GCF_000024605.1:WP_015738271.1 550 ML 551
                                               86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (552 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: 10.10
//
[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