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.371930.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 30.24
//
[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:

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:

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:

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:

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