GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Flavobacterium glycines Gm-149

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_066328412.1 BLR17_RS00950 3-isopropylmalate dehydratase large subunit

Query= uniprot:A0A1X9Z7T5
         (470 letters)



>NCBI__GCF_900100165.1:WP_066328412.1
          Length = 464

 Score =  633 bits (1633), Expect = 0.0
 Identities = 302/465 (64%), Positives = 368/465 (79%), Gaps = 1/465 (0%)

Query: 1   MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVAT 60
           MSKTL +K+WD+HVV+  E  PD+ +ID H IHEVTSP AF GL+ RG+ V  P++T AT
Sbjct: 1   MSKTLFDKVWDSHVVRKIEDGPDVFFIDRHFIHEVTSPVAFLGLKTRGVSVLYPERTFAT 60

Query: 61  ADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLP 120
           ADHN PT+NQ LP+ + LS  Q+  L  N AE+G+  +GLGH   GIVHV+GPE GITLP
Sbjct: 61  ADHNTPTINQHLPVADALSANQLKALETNAAEYGISHWGLGHQKNGIVHVVGPENGITLP 120

Query: 121 GKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGA 180
           G T+VCGDSHTSTHGAFGAIAFGIGTS+VE V +TQC++Q KPK M+I VNG+L KGV  
Sbjct: 121 GATIVCGDSHTSTHGAFGAIAFGIGTSEVEMVLSTQCIMQPKPKKMRINVNGKLSKGVTP 180

Query: 181 KDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTF 240
           KD+ LYIIA+++ +GGTGYF+EYAG+  E ++ME RMT+CN+SIEMGARGG+IAPDQTTF
Sbjct: 181 KDVALYIIAQLTTSGGTGYFVEYAGNVFEEMTMEGRMTVCNLSIEMGARGGMIAPDQTTF 240

Query: 241 DYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGI 300
           D+++GR +AP GE W KA+ YWKTL +D DA FD+ L   A DI PMITYGTNPGMG+GI
Sbjct: 241 DFLEGRLYAPKGEAWTKAVEYWKTLKTDTDAVFDAELNIKAEDIEPMITYGTNPGMGIGI 300

Query: 301 QEHIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADF 360
            +HIP+   Q E  + +Y+K+L+YMGF +D  +IGKP+DYVF+GSCTN RIED R  A  
Sbjct: 301 TKHIPSAD-QVEGGEETYKKSLNYMGFHEDDVMIGKPIDYVFLGSCTNGRIEDFRAFASI 359

Query: 361 VKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAG 420
           VK ++KADNVT W+VPGS  VE Q K EG+  I   AGF LR+PGCSACL MN+DK+PAG
Sbjct: 360 VKGRKKADNVTAWLVPGSHVVEAQIKEEGILDILTEAGFVLRQPGCSACLAMNDDKVPAG 419

Query: 421 KYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDLL 465
           KY VSTSNRNFEGRQG  +RTLLASP+ AAAAAVTGK+TD RDLL
Sbjct: 420 KYAVSTSNRNFEGRQGPGSRTLLASPIMAAAAAVTGKLTDPRDLL 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: 647
Number of extensions: 17
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: 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 WP_066328412.1 BLR17_RS00950 (3-isopropylmalate dehydratase large subunit)
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.2886858.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-198  643.4   0.1   1.1e-197  643.2   0.1    1.0  1  NCBI__GCF_900100165.1:WP_066328412.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066328412.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.2   0.1  1.1e-197  1.1e-197       1     465 [.       1     462 [.       1     463 [. 0.99

  Alignments for each domain:
  == domain 1  score: 643.2 bits;  conditional E-value: 1.1e-197
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m+ktl++k++d+hvv++ e+++d+++idrh++hevtsp af gl+++g  v  +++t+at dhn +t ++ + 
  NCBI__GCF_900100165.1:WP_066328412.1   1 MSKTLFDKVWDSHVVRKIEDGPDVFFIDRHFIHEVTSPVAFLGLKTRGVSVLYPERTFATADHNTPTINQHLP 73 
                                           79*********************************************************************** PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           + +  +  q+k+le n+ e+g+  ++l ++++givhvvgpe+g+tlpg tivcgdsht+thgafga+afgigt
  NCBI__GCF_900100165.1:WP_066328412.1  74 VADALSANQLKALETNAAEYGISHWGLGHQKNGIVHVVGPENGITLPGATIVCGDSHTSTHGAFGAIAFGIGT 146
                                           ************************************************************************* PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           seve vl+tq ++q ++k+++i+v+gkl+kg+t kd+ l+ii +++++ggtgy ve+ag+++++++me+rmtv
  NCBI__GCF_900100165.1:WP_066328412.1 147 SEVEMVLSTQCIMQPKPKKMRINVNGKLSKGVTPKDVALYIIAQLTTSGGTGYFVEYAGNVFEEMTMEGRMTV 219
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cn++ie+ga+ g+iapd+ttf+++ +r yapkg+ + kav+ywktlktd +a+fd +++++a+di p++t+gt
  NCBI__GCF_900100165.1:WP_066328412.1 220 CNLSIEMGARGGMIAPDQTTFDFLEGRLYAPKGEAWTKAVEYWKTLKTDTDAVFDAELNIKAEDIEPMITYGT 292
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           npg+ + +++++p+ +++      ++ +k+l+y+g++ +  +    +d vf+gsctn+ried+ra a++vkg+
  NCBI__GCF_900100165.1:WP_066328412.1 293 NPGMGIGITKHIPSADQVEGGE--ETYKKSLNYMGFHEDDVMIGKPIDYVFLGSCTNGRIEDFRAFASIVKGR 363
                                           **************99997654..56789******************************************** PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                           k+adnv  a +vpgs  v +q ++eg+  i+ eagf  r++gcs cl+mn+d++++++   stsnrnfegrqg
  NCBI__GCF_900100165.1:WP_066328412.1 364 KKADNVT-AWLVPGSHVVEAQIKEEGILDILTEAGFVLRQPGCSACLAMNDDKVPAGKYAVSTSNRNFEGRQG 435
                                           ******9.999************************************************************** PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465
                                            g+rt l sp maaaaav+gk+ d r+
  NCBI__GCF_900100165.1:WP_066328412.1 436 PGSRTLLASPIMAAAAAVTGKLTDPRD 462
                                           ************************997 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.00
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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