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

GapMind for Amino acid biosynthesis

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

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate 351388 BT1860 3-isopropylmalate dehydratase large subunit (NCBI ptt file)

Query= uniprot:A0A1X9Z7T5
         (470 letters)



>FitnessBrowser__Btheta:351388
          Length = 464

 Score =  625 bits (1612), Expect = 0.0
 Identities = 298/462 (64%), Positives = 365/462 (79%)

Query: 4   TLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVATADH 63
           TL +KIWDAHVV + E  P  LYID    HEVTSPQAF GLR+RG+ V RP++     DH
Sbjct: 3   TLFDKIWDAHVVTTVEDGPTQLYIDRLYCHEVTSPQAFAGLRERGIKVLRPEKVFCMPDH 62

Query: 64  NVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLPGKT 123
           N PT +Q  PI++ +S+ QVD LTKN  +FG+  +G+ HP  GI+HV+GPE  +TLPG T
Sbjct: 63  NTPTHDQDKPIEDPISKTQVDTLTKNAKDFGLTHFGMMHPKNGIIHVVGPERALTLPGMT 122

Query: 124 MVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGAKDI 183
           +VCGDSHTSTHGA GAIAFGIGTS+VE V A+QC+LQS+PKTM+I V+GELGKGV AKD+
Sbjct: 123 IVCGDSHTSTHGAMGAIAFGIGTSEVEMVLASQCILQSRPKTMRITVDGELGKGVTAKDV 182

Query: 184 ILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTFDYI 243
            LY+++K++ +G TGYF+EYAGSAI  L+ME R+T+CN+SIEMGARGG++APD+ TF+YI
Sbjct: 183 ALYMMSKMTTSGATGYFVEYAGSAIRNLTMEGRLTLCNLSIEMGARGGMVAPDEVTFEYI 242

Query: 244 KGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGIQEH 303
           KGRE AP GE WD+A+ YWKTL SD DA FD  + FDAADI PMITYGTNPGMGMGI ++
Sbjct: 243 KGRENAPQGEAWDQAMEYWKTLKSDDDAVFDQEVRFDAADIEPMITYGTNPGMGMGITQN 302

Query: 304 IPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADFVKD 363
           IP T    E  ++S++K+++YMGF    SL+GK +DYVF+G+CTN RIED R  A  VK 
Sbjct: 303 IPTTEGMGEAAQVSFKKSMEYMGFQPGESLLGKKIDYVFLGACTNGRIEDFRAFASLVKG 362

Query: 364 KRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAGKYC 423
           +RKADNV  W+VPGS  V+ Q + EG+DKI   AGF +R+PGCSACL MN+DKIPAGKY 
Sbjct: 363 RRKADNVIAWLVPGSWMVDAQIRKEGIDKILTEAGFAIRQPGCSACLAMNDDKIPAGKYS 422

Query: 424 VSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDLL 465
           VSTSNRNFEGRQG  ARTLLASPL AAAAAVTG ITD R+L+
Sbjct: 423 VSTSNRNFEGRQGPGARTLLASPLVAAAAAVTGVITDPRELM 464


Lambda     K      H
   0.317    0.135    0.399 

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: 658
Number of extensions: 21
Number of successful extensions: 1
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: 470
Length of database: 464
Length adjustment: 33
Effective length of query: 437
Effective length of database: 431
Effective search space:   188347
Effective search space used:   188347
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 351388 BT1860 (3-isopropylmalate dehydratase large subunit (NCBI ptt file))
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.24553.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.1e-197  642.3   0.1   2.3e-197  642.1   0.1    1.0  1  lcl|FitnessBrowser__Btheta:351388  BT1860 3-isopropylmalate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351388  BT1860 3-isopropylmalate dehydratase large subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.1   0.1  2.3e-197  2.3e-197       3     465 ..       2     462 ..       1     463 [. 0.99

  Alignments for each domain:
  == domain 1  score: 642.1 bits;  conditional E-value: 2.3e-197
                          TIGR00170   3 ktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeek 78 
                                        +tl++k++dahvv   e++++ lyidr   hevtspqaf glr++g kv r++k ++  dhn +t+ +d  i +  
  lcl|FitnessBrowser__Btheta:351388   2 NTLFDKIWDAHVVTTVEDGPTQLYIDRLYCHEVTSPQAFAGLRERGIKVLRPEKVFCMPDHNTPTHDQDKPIEDPI 77 
                                        69************************************************************************** PP

                          TIGR00170  79 aklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvla 154
                                        +k qv +l+kn+k+fg+  f++ + ++gi+hvvgpe+ ltlpg+tivcgdsht+thga+ga+afgigtseve vla
  lcl|FitnessBrowser__Btheta:351388  78 SKTQVDTLTKNAKDFGLTHFGMMHPKNGIIHVVGPERALTLPGMTIVCGDSHTSTHGAMGAIAFGIGTSEVEMVLA 153
                                        **************************************************************************** PP

                          TIGR00170 155 tqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagaka 230
                                        +q + q+r+kt++i+v+g+l kg+takd+ l+++ k++++g tgy ve+ag air+l+me+r+t+cn++ie+ga+ 
  lcl|FitnessBrowser__Btheta:351388 154 SQCILQSRPKTMRITVDGELGKGVTAKDVALYMMSKMTTSGATGYFVEYAGSAIRNLTMEGRLTLCNLSIEMGARG 229
                                        **************************************************************************** PP

                          TIGR00170 231 gliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpd 306
                                        g++apde+tfey+k+r+ ap+g+ +++a++ywktlk+d++a+fd++v ++a di p++t+gtnpg+ + +++++p 
  lcl|FitnessBrowser__Btheta:351388 230 GMVAPDEVTFEYIKGRENAPQGEAWDQAMEYWKTLKSDDDAVFDQEVRFDAADIEPMITYGTNPGMGMGITQNIPT 305
                                        **************************************************************************** PP

                          TIGR00170 307 pksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsgl 382
                                         + + +   + s +k+++y+g++pg +l   k+d vf+g+ctn+ried+ra a++vkg+++adnv  a +vpgs +
  lcl|FitnessBrowser__Btheta:351388 306 TEGMGEA-AQVSFKKSMEYMGFQPGESLLGKKIDYVFLGACTNGRIEDFRAFASLVKGRRKADNVI-AWLVPGSWM 379
                                        ***9876.56789****************************************************9.999****** PP

                          TIGR00170 383 vkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavag 458
                                        v +q  keg+dki+ eagf  r++gcs cl+mn+d++++++   stsnrnfegrqg gart l sp +aaaaav+g
  lcl|FitnessBrowser__Btheta:351388 380 VDAQIRKEGIDKILTEAGFAIRQPGCSACLAMNDDKIPAGKYSVSTSNRNFEGRQGPGARTLLASPLVAAAAAVTG 455
                                        **************************************************************************** PP

                          TIGR00170 459 kfvdire 465
                                         + d re
  lcl|FitnessBrowser__Btheta:351388 456 VITDPRE 462
                                        **99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (464 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: 00:00:00.02
# Mc/sec: 7.72
//
[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