Alignments for a candidate for ilvC in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Bacteroides thetaiotaomicron VPI-5482

Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; EC 1.1.1.382 (characterized)
to candidate 351602 BT2074 ketol-acid reductoisomerase (NCBI ptt file)

Query= SwissProt::A8ZTR0
         (352 letters)



>FitnessBrowser__Btheta:351602
          Length = 359

 Score =  457 bits (1177), Expect = e-133
 Identities = 225/347 (64%), Positives = 270/347 (77%), Gaps = 1/347 (0%)

Query: 1   MPTINFGGVEENVVTSEEFTLKKAREVLKNEVITVLGYGVQGPAQALNLKDNGFEVIIGQ 60
           M  +NFGG  ENVV  +EF L+KAREVLKNE I V+GYGVQGP QALNL+DNGF VI+GQ
Sbjct: 13  MAQLNFGGTVENVVIRDEFPLEKAREVLKNETIAVIGYGVQGPGQALNLRDNGFNVIVGQ 72

Query: 61  LEGDAYWEKAIADGFVPGKTLFPIEEAAKKGTIIKMLLSDAGQVAVWPKVKKCLKKGDAL 120
            +G  Y +KA+ADG+VPG+TLF IEEA +KGTII  LLSDA  ++VWP +K  L  G AL
Sbjct: 73  RQGKTY-DKAVADGWVPGETLFGIEEACEKGTIIMCLLSDAAVMSVWPTIKPYLTAGKAL 131

Query: 121 YFSHGFGIVYKDQTGIVPPKNVDVILVAPKGSGTNVRRNFKDGSGINSSYAVFQDATGRA 180
           YFSHGF I + D+TG+VPP ++DVI+VAPKGSGT++R  F +G G+NSSYA++QDATG A
Sbjct: 132 YFSHGFAITWSDRTGVVPPADIDVIMVAPKGSGTSLRTMFLEGRGLNSSYAIYQDATGNA 191

Query: 181 EERTIALGIAIGSGYLFPTTFEKEVFSDLTGERGVLMGCLAGTMEAQYNVLRKHGHSPSE 240
            +RTIALGI IGSGYLF TTF +E  SDLTGERG LMG + G + AQY VLR++GH+PSE
Sbjct: 192 MDRTIALGIGIGSGYLFETTFIREATSDLTGERGSLMGAIQGLLLAQYEVLRENGHTPSE 251

Query: 241 AFNETVEELTQSLIRLVAENGMDWMFANCSTTAQRGALDWAPKFRDAVAPVFDSLYRRVK 300
           AFNETVEELTQSL+ L A+NGMDWM+ANCSTTAQRGALDW   F DA+ PV + LY  VK
Sbjct: 252 AFNETVEELTQSLMPLFAKNGMDWMYANCSTTAQRGALDWMGPFHDAIKPVVEKLYHSVK 311

Query: 301 NGAETRRVLKVNSAPNYLEKLRKELDTIKNSEMWQAGAAVRALRPEN 347
            G E +  +  NS P+Y EKL +EL  ++ SEMWQ    VR LRPEN
Sbjct: 312 TGNEAQISIDSNSKPDYREKLEEELKALRESEMWQTAVTVRKLRPEN 358


Lambda     K      H
   0.316    0.134    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: 443
Number of extensions: 11
Number of successful extensions: 2
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: 352
Length of database: 359
Length adjustment: 29
Effective length of query: 323
Effective length of database: 330
Effective search space:   106590
Effective search space used:   106590
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: 49 (23.5 bits)

Align candidate 351602 BT2074 (ketol-acid reductoisomerase (NCBI ptt file))
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.5018.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.7e-98  315.4   0.0    1.9e-98  315.2   0.0    1.0  1  lcl|FitnessBrowser__Btheta:351602  BT2074 ketol-acid reductoisomera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351602  BT2074 ketol-acid reductoisomerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.2   0.0   1.9e-98   1.9e-98       1     313 [.      40     358 ..      40     359 .] 0.96

  Alignments for each domain:
  == domain 1  score: 315.2 bits;  conditional E-value: 1.9e-98
                          TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeed....GfkvltveeaikkadlimiLlpDevq 72 
                                        lk++++a+iGyG qG +qalnlrd+g nvivg r++ ++++kA  d    G  ++ +eea +k+ +im Ll+D++ 
  lcl|FitnessBrowser__Btheta:351602  40 LKNETIAVIGYGVQGPGQALNLRDNGFNVIVGQRQG-KTYDKAVADgwvpGETLFGIEEACEKGTIIMCLLSDAAV 114
                                        799*****************************9988.9********8888899*********************** PP

                          TIGR00465  73 kevyeaeikpllkegkallfsHGfnivfkqiv...ipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtg 145
                                         +v+   ikp+l++gkal+fsHGf i +++ +   +p+d+dv++vAPKg+G+ +R ++ egrG++s++A++qd+tg
  lcl|FitnessBrowser__Btheta:351602 115 MSVWPT-IKPYLTAGKALYFSHGFAITWSDRTgvvPPADIDVIMVAPKGSGTSLRTMFLEGRGLNSSYAIYQDATG 189
                                        ****99.*******************997654444***************************************** PP

                          TIGR00465 146 eakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhel.kl 220
                                        +a++   a+  +iG++  +++ettF +E  sDL GE++ L+G +++l++a++++L+e+G+ p++A++e+v+el ++
  lcl|FitnessBrowser__Btheta:351602 190 NAMDRTIALGIGIGSG--YLFETTFIREATSDLTGERGSLMGAIQGLLLAQYEVLRENGHTPSEAFNETVEELtQS 263
                                        *********9999999..*******************************************************9** PP

                          TIGR00465 221 ivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagkpafeearkke.. 294
                                        +++l  ++G++ m+ ++s+tA++gal++   +++++k++++k+++++++G++a+  ++++ ++kp+++e+ + e  
  lcl|FitnessBrowser__Btheta:351602 264 LMPLFAKNGMDWMYANCSTTAQRGALDWMGPFHDAIKPVVEKLYHSVKTGNEAQ-ISIDS-NSKPDYREKLEEElk 337
                                        *****************************************************9.66665.9********999999 PP

                          TIGR00465 295 ..keqeiekvGkelralvkae 313
                                          +e e++++ +++r+l++++
  lcl|FitnessBrowser__Btheta:351602 338 alRESEMWQTAVTVRKLRPEN 358
                                        99**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (359 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.79
//
[ok]

This GapMind analysis is from Apr 09 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