GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pseudomonas fluorescens FW300-N1B4

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Pf1N1B4_15 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15
          Length = 472

 Score =  594 bits (1531), Expect = e-174
 Identities = 300/468 (64%), Positives = 363/468 (77%), Gaps = 5/468 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL+D+H+V + ++ + L+YIDRH++HEVTSPQAF+GLR  GR   +     AT D
Sbjct: 4   KTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPD 63

Query: 63  HNVSTQTK---DINAC-GEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
           HNV T  +    I+A   +++R+Q+Q L  NC E+G+  + +N   QGIVHV+GPEQG T
Sbjct: 64  HNVPTTAERKGGIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L   + K M + V+G+   G+
Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVSVEGQLPFGV 183

Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238
           TAKDIVLA+IGK G+AGG GH +EF G AIRDLS+EGRMT+CNM+IE GA+ GLVA DE 
Sbjct: 184 TAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADEK 243

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
           T  YVKGR  APKG ++D AV  WK L +D  A FDT+V L A +I PQV+WGT+P  V+
Sbjct: 244 TVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADAKFDTIVELDATQIKPQVSWGTSPEMVL 303

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
           +V+ N+PDPA   D V+R S E+AL YMGL     +T++ +D+VFIGSCTNSRIEDLRAA
Sbjct: 304 AVDQNVPDPAKEMDLVKRGSIERALKYMGLTANQAITDIQLDRVFIGSCTNSRIEDLRAA 363

Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           A IAKGRKVA  + QA+VVPGSG VKAQAE+EGLDKIF+EAGFEWR PGCSMCLAMN DR
Sbjct: 364 AVIAKGRKVASTIKQAIVVPGSGLVKAQAESEGLDKIFLEAGFEWREPGCSMCLAMNPDR 423

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           L  GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAV G F D+R +
Sbjct: 424 LESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVNGRFVDVREL 471


Lambda     K      H
   0.317    0.134    0.396 

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: 744
Number of extensions: 23
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: 466
Length of database: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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 Pf1N1B4_15 (3-isopropylmalate dehydratase large subunit (EC 4.2.1.33))
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.2984106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     3e-237  773.6   1.8   3.7e-237  773.3   1.8    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15  3-isopropylmalate dehydratase la


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15  3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  773.3   1.8  3.7e-237  3.7e-237       2     466 .]       3     471 ..       2     471 .. 0.99

  Alignments for each domain:
  == domain 1  score: 773.3 bits;  conditional E-value: 3.7e-237
                                    TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnist 67 
                                                   ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk  r+d  +at dhn++t
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15   3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPDHNVPT 68 
                                                  59***************************************************************9 PP

                                    TIGR00170  68 esr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgds 129
                                                  ++        i++++++lqv++l+ n++e+g+  f +++++qgivhv+gpe+g tlpg+t+vcgds
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15  69 TAErkggIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDS 134
                                                  87656753358899**************************************************** PP

                                    TIGR00170 130 htathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvag 195
                                                  ht+thgafgala gigtsevehvlatq l+ ++ k++ + veg+l  g+takdi+la+igkig+ag
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 135 HTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVSVEGQLPFGVTAKDIVLAVIGKIGTAG 200
                                                  ****************************************************************** PP

                                    TIGR00170 196 gtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavay 261
                                                  g g+ +efag airdls+e+rmt+cnm+ieaga+ gl+a de t +yvk+r++apkg+e++ av+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 201 GNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADEKTVAYVKGRPFAPKGAEWDLAVEA 266
                                                  ****************************************************************** PP

                                    TIGR00170 262 wktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylg 327
                                                  wk l +d +akfd+ v l+a++i pqv+wgt+p++vl+v+++vpdp++  d v++ s+e+al+y+g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 267 WKDLVSDADAKFDTIVELDATQIKPQVSWGTSPEMVLAVDQNVPDPAKEMDLVKRGSIERALKYMG 332
                                                  ****************************************************************** PP

                                    TIGR00170 328 lepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegld 393
                                                  l++++ ++di++d+vfigsctnsriedlraaa ++kg+kva+++k+a+vvpgsglvk+qae egld
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 333 LTANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAIVVPGSGLVKAQAESEGLD 398
                                                  ****************************************************************** PP

                                    TIGR00170 394 kifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagk 459
                                                  kifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg+g+rthlvspamaaaaav+g+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 399 KIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVNGR 464
                                                  ****************************************************************** PP

                                    TIGR00170 460 fvdirel 466
                                                  fvd+rel
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_15 465 FVDVREL 471
                                                  *****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (472 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: 00:00:00.01
# Mc/sec: 20.30
//
[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