Alignments for a candidate for leuC in Pseudomonas putida KT2440

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.29837.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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.01
//
[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