Alignments for a candidate for ilvI in Calditerrivibrio nitroreducens DSM 19672

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Calditerrivibrio nitroreducens DSM 19672

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013450956.1 CALNI_RS04160 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000183405.1:WP_013450956.1
          Length = 565

 Score =  595 bits (1534), Expect = e-174
 Identities = 303/565 (53%), Positives = 390/565 (69%), Gaps = 10/565 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GAEILV  L +  V+ ++GYPGG +L+IYD L   +   H+L RHEQ  +HAADGYAR+T
Sbjct: 5   GAEILVECLKKHKVDLIFGYPGGVLLHIYDRLF-DSDILHVLPRHEQGGIHAADGYARST 63

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGV   TSGPG TN VTGIATAYLDS+P+VV TG V TH IG DAFQE D VGITRPI
Sbjct: 64  GKVGVCFGTSGPGATNLVTGIATAYLDSVPLVVFTGQVSTHLIGGDAFQEADIVGITRPI 123

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV----SRNACKYEYPKSIDMR 196
           VKH++LVKDV DLA TI +AF++A TGRPGPV+VD+PKDV    S+N C  +    I + 
Sbjct: 124 VKHSYLVKDVDDLAPTIAEAFYLAKTGRPGPVLVDLPKDVIAAKSKNLCSTD----IKLV 179

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
            YNP  +GH  QI+K + +L+ A+ P +  GGGV  +NA +EL++       PV ++LMG
Sbjct: 180 GYNPTYEGHPMQIKKMLKMLENAKAPVVLIGGGVKWSNAHEELKKFVETLNLPVVSSLMG 239

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           +GAFP   K +VG  GMHG Y +NMA+   D ++AIG RF DR  G    +  +A+K   
Sbjct: 240 IGAFPNPHKNWVGWAGMHGNYASNMALTEADFILAIGTRFSDRTTGRLDAYAPKAKK-AQ 298

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           IDIDP+SI K VKVD PIVG+ K VL +++  IK  +    +     W ++IE W +   
Sbjct: 299 IDIDPTSIDKNVKVDTPIVGDCKTVLNQILNYIKDFNWDKCKNDREDWLKKIEYWDNERP 358

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
             Y  S +IIKPQ+VVEKI+E+T GDA I ++VGQ+QMWAAQFYKF +PR++I SGGLGT
Sbjct: 359 FSYKFSDKIIKPQFVVEKIYEVTNGDAIITTEVGQNQMWAAQFYKFKDPRQFITSGGLGT 418

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG G P A+G K   P +EV  I G+GS  M +QEL T +QY   VK+  LNN +LGM+R
Sbjct: 419 MGYGFPAAIGAKLGNPNREVFDIAGDGSFLMNMQELCTAVQYRVGVKVAILNNKFLGMIR 478

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           QWQ + Y+ RYS+S ++  PDFVKLA+AYG VG +V   SDVEP LRE+ ++KD+ V  D
Sbjct: 479 QWQHLFYNKRYSYSCLECQPDFVKLADAYGCVGFQVANPSDVEPVLRESLKIKDKPVLFD 538

Query: 557 FQTDPTENVWPMVQAGKGISEMLLG 581
           F  D  ENV+PMV AG  ++EM+ G
Sbjct: 539 FLVDREENVYPMVPAGAALNEMIYG 563


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: 951
Number of extensions: 35
Number of successful extensions: 3
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: 565
Length adjustment: 36
Effective length of query: 549
Effective length of database: 529
Effective search space:   290421
Effective search space used:   290421
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_013450956.1 CALNI_RS04160 (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.24202.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-254  831.1   0.0   2.4e-254  830.9   0.0    1.0  1  lcl|NCBI__GCF_000183405.1:WP_013450956.1  CALNI_RS04160 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013450956.1  CALNI_RS04160 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.9   0.0  2.4e-254  2.4e-254       2     554 ..       4     561 ..       3     564 .. 0.98

  Alignments for each domain:
  == domain 1  score: 830.9 bits;  conditional E-value: 2.4e-254
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +gaeilve lkk++v+ +fGyPGG +l+iyd+l+ds++ h+l+rheq+ +haadGyar++GkvGv+++t
  lcl|NCBI__GCF_000183405.1:WP_013450956.1   4 TGAEILVECLKKHKVDLIFGYPGGVLLHIYDRLFDSDILHVLPRHEQGGIHAADGYARSTGKVGVCFGT 72 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtgiatayldsvPlvv+tGqv+t+liG dafqe+di+Git+p++khs+lvk+++dl+ ++ 
  lcl|NCBI__GCF_000183405.1:WP_013450956.1  73 SGPGATNLVTGIATAYLDSVPLVVFTGQVSTHLIGGDAFQEADIVGITRPIVKHSYLVKDVDDLAPTIA 141
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf++a+tGrPGPvlvdlPkdv +a+ ++  +++++l gy+pt +gh++qikk l+++e+ak Pv+l+G
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 142 EAFYLAKTGRPGPVLVDLPKDVIAAKSKNLCSTDIKLVGYNPTYEGHPMQIKKMLKMLENAKAPVVLIG 210
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGv  ++a+eelk+++e+l++pv+++l+G+Gafp+ h++ +g +GmhG +++n+a++ead ++a+G+rf
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 211 GGVKWSNAHEELKKFVETLNLPVVSSLMGIGAFPNPHKNWVGWAGMHGNYASNMALTEADFILAIGTRF 279
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wle 341
                                               +dr+tg l+ +ap+ak   ididP++i+knvkvd pivGd+k+vl+++l+ +k+      k+++e Wl+
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 280 SDRTTGRLDAYAPKAKKAQIDIDPTSIDKNVKVDTPIVGDCKTVLNQILNYIKDFnwdkCKNDREdWLK 348
                                               **************************************************9998777763444445*** PP

                                 TIGR00118 342 kieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlG 410
                                               kie w +e +++++ +++ ikPq v+++++++++++ai+tt+vGq+qmwaaqfyk+k pr+fitsgGlG
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 349 KIEYWDNERPFSYKFSDKIIKPQFVVEKIYEVTNGDAIITTEVGQNQMWAAQFYKFKDPRQFITSGGLG 417
                                               ********************************************************************* PP

                                 TIGR00118 411 tmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfye 479
                                               tmG+G+Paa+Gak+++p+ +v +++Gdgsf mn+qel t+v+y + vk+ ilnn++lGm++qWq+lfy+
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 418 TMGYGFPAAIGAKLGNPNREVFDIAGDGSFLMNMQELCTAVQYRVGVKVAILNNKFLGMIRQWQHLFYN 486
                                               ********************************************************************* PP

                                 TIGR00118 480 erysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapG 547
                                               +rys ++l++ +pdfvkla+ayG +g ++++p+++e  l+e l+ k +pvl+d+ vd+ee+v+Pmv+ G
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 487 KRYSYSCLEC-QPDFVKLADAYGCVGFQVANPSDVEPVLRESLKIKdKPVLFDFLVDREENVYPMVPAG 554
                                               *********8.********************************98879********************* PP

                                 TIGR00118 548 agldelv 554
                                               a+l+e++
  lcl|NCBI__GCF_000183405.1:WP_013450956.1 555 AALNEMI 561
                                               ******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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: 7.11
//
[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