Alignments for a candidate for leuC in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Pseudomonas fluorescens GW456-L13

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate PfGW456L13_3948 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948
          Length = 472

 Score =  592 bits (1527), 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  HNVPTTPERKGGIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L   + K M + V+G+   G+
Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGQLPFGV 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  ATFDTVV L A +I PQV+WGT+P  V+
Sbjct: 244 TVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADATFDTVVELDATQIKPQVSWGTSPEMVL 303

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
           +V+ N+PDPA   D V+R S  +AL YMGL     +T++ +D+VFIGSCTNSRIEDLRAA
Sbjct: 304 AVDQNVPDPAKEMDLVKRDSIVRALKYMGLTANQAITDIQLDRVFIGSCTNSRIEDLRAA 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 GGRTHLVSPAMAAAAA+ G F D+R +
Sbjct: 424 LESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAINGRFVDVREL 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: 746
Number of extensions: 25
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 PfGW456L13_3948 (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.24098.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.4e-237  774.0   1.5   2.9e-237  773.7   1.5    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948  3-isopropylmalate dehydratase la


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948  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 !  773.7   1.5  2.9e-237  2.9e-237       2     466 .]       3     471 ..       2     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 773.7 bits;  conditional E-value: 2.9e-237
                                               TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdk 56 
                                                              ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk  r+d 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948   3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDA 57 
                                                             59***************************************************** PP

                                               TIGR00170  57 tlatldhnistesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgi 107
                                                              +at dhn++t+         i++++++lqv++l+ n++e+g+  f +++++qgi
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948  58 NIATPDHNVPTTPErkggIDAIVDQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGI 112
                                                             **********986546743357899****************************** PP

                                               TIGR00170 108 vhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlatqtlkqar 162
                                                             vhv+gpe+g tlpg+t+vcgdsht+thgafgala gigtsevehvlatq l+ ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 113 VHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKK 167
                                                             ******************************************************* PP

                                               TIGR00170 163 aktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                                              k++ ++veg+l  g+takdi+la+igkig+agg g+ +efag airdls+e+rm
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 168 MKNMLVRVEGQLPFGVTAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRDLSVEGRM 222
                                                             ******************************************************* PP

                                               TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegak 272
                                                             t+cnm+ieaga+ gl+a de t +yvk+r++apkg+e++ av+ wk l +d +a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 223 TICNMSIEAGARVGLVAADEKTVAYVKGRPFAPKGAEWDLAVEAWKDLVSDADAT 277
                                                             ******************************************************* PP

                                               TIGR00170 273 fdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylg 327
                                                             fd+vv l+a++i pqv+wgt+p++vl+v+++vpdp++  d v++ s+ +al+y+g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 278 FDTVVELDATQIKPQVSWGTSPEMVLAVDQNVPDPAKEMDLVKRDSIVRALKYMG 332
                                                             ******************************************************* PP

                                               TIGR00170 328 lepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsgl 382
                                                             l++++ ++di++d+vfigsctnsriedlraaa ++kg+kva+++k+a+vvpgsgl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 333 LTANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAIVVPGSGL 387
                                                             ******************************************************* PP

                                               TIGR00170 383 vkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrq 437
                                                             vk+qae egldkifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrq
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 388 VKAQAESEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQ 442
                                                             ******************************************************* PP

                                               TIGR00170 438 gkgarthlvspamaaaaavagkfvdirel 466
                                                             g+g+rthlvspamaaaaa++g+fvd+rel
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3948 443 GAGGRTHLVSPAMAAAAAINGRFVDVREL 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.18
//
[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