GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pseudomonas putida KT2440

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate PP_1985 PP_1985 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Putida:PP_1985
          Length = 477

 Score =  593 bits (1528), Expect = e-174
 Identities = 299/468 (63%), Positives = 361/468 (77%), Gaps = 5/468 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL++AH V   ++ + L+YIDRH++HEVTSPQAF+GLR   R   +     AT D
Sbjct: 4   KTLYDKLWEAHEVKRRDDGSSLIYIDRHIIHEVTSPQAFEGLRLANRKPWRIDANIATPD 63

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

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

Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238
           TAKDIVLA+IGK G+AGG GH +EF G AIR+LSMEGRMT+CNM+IE GA+ GLVA D T
Sbjct: 184 TAKDIVLAVIGKIGTAGGNGHAMEFAGSAIRELSMEGRMTICNMSIEAGARVGLVATDAT 243

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
           T  YV+GR +APKG+ +  AV  WK L +D+ A FDTVV L A +I PQV+WGT+P  V+
Sbjct: 244 TVAYVEGRPYAPKGEQWKQAVESWKDLVSDDDAVFDTVVELDASQIKPQVSWGTSPEMVL 303

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

Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           AEIAKGRKVA  V QA+VVPGSG VKAQAE EGLDKIF+EAGFEWR PGCSMCLAMN DR
Sbjct: 364 AEIAKGRKVAASVKQAIVVPGSGLVKAQAEREGLDKIFLEAGFEWREPGCSMCLAMNPDR 423

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           L  GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAV GHF D+R +
Sbjct: 424 LESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVAGHFIDVREL 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: 730
Number of extensions: 17
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: 477
Length adjustment: 33
Effective length of query: 433
Effective length of database: 444
Effective search space:   192252
Effective search space used:   192252
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 PP_1985 PP_1985 (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.4874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-236  771.5   1.7   1.7e-236  771.2   1.7    1.0  1  lcl|FitnessBrowser__Putida:PP_1985  PP_1985 3-isopropylmalate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1985  PP_1985 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  771.2   1.7  1.7e-236  1.7e-236       2     466 .]       3     471 ..       2     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 771.2 bits;  conditional E-value: 1.7e-236
                           TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr....dv 72 
                                          ktly+kl++ah vk+ +++++l+yidrh++hevtspqafeglr a+rk  r+d  +at dhn++t+        
  lcl|FitnessBrowser__Putida:PP_1985   3 GKTLYDKLWEAHEVKRRDDGSSLIYIDRHIIHEVTSPQAFEGLRLANRKPWRIDANIATPDHNVPTTPErkggIE 77 
                                         59***************************************************************9865466334 PP

                           TIGR00170  73 eikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147
                                          i++++++lqv++l++n++e+g+  f +++++qgivhv+ pe+g tlpg+t+vcgdsht+thgafgala gigts
  lcl|FitnessBrowser__Putida:PP_1985  78 AIVDQVSRLQVQTLDENCDEYGIVEFKMNDERQGIVHVISPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGTS 152
                                         6789*********************************************************************** PP

                           TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnm 222
                                         evehvlatq l+ ++ k++ ++veg+l  g+takdi+la+igkig+agg g+ +efag air+lsme+rmt+cnm
  lcl|FitnessBrowser__Putida:PP_1985 153 EVEHVLATQCLVAKKMKNMLVRVEGQLPAGVTAKDIVLAVIGKIGTAGGNGHAMEFAGSAIRELSMEGRMTICNM 227
                                         *************************************************************************** PP

                           TIGR00170 223 aieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqv 297
                                         +ieaga+ gl+a d tt +yv +r+yapkg+++++av+ wk l +d++a+fd+vv l+a++i pqv+wgt+p++v
  lcl|FitnessBrowser__Putida:PP_1985 228 SIEAGARVGLVATDATTVAYVEGRPYAPKGEQWKQAVESWKDLVSDDDAVFDTVVELDASQIKPQVSWGTSPEMV 302
                                         *************************************************************************** PP

                           TIGR00170 298 lsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvk 372
                                         l+v++ vpdp+  +d v++ s+e+al+y+gl++++ ++dik+d+vfigsctnsriedlraaae++kg+kva +vk
  lcl|FitnessBrowser__Putida:PP_1985 303 LAVDQRVPDPAAETDLVKRGSIERALKYMGLTANQAITDIKLDRVFIGSCTNSRIEDLRAAAEIAKGRKVAASVK 377
                                         *************************************************************************** PP

                           TIGR00170 373 lalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvs 447
                                         +a+vvpgsglvk+qae+egldkifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg+g+rthlvs
  lcl|FitnessBrowser__Putida:PP_1985 378 QAIVVPGSGLVKAQAEREGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQGAGGRTHLVS 452
                                         *************************************************************************** PP

                           TIGR00170 448 pamaaaaavagkfvdirel 466
                                         pamaaaaavag+f+d+rel
  lcl|FitnessBrowser__Putida:PP_1985 453 PAMAAAAAVAGHFIDVREL 471
                                         *****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (477 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: 10.97
//
[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