GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pseudomonas fluorescens FW300-N2C3

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate AO356_21400 AO356_21400 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_21400
          Length = 472

 Score =  593 bits (1530), Expect = e-174
 Identities = 301/468 (64%), Positives = 361/468 (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---DINACGE-MARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
           HNV T  +    I A  + ++R+Q+Q L  NC E+G+  + +N   QGIVHV+GPEQG T
Sbjct: 64  HNVPTTPERKGGIEAIADQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L   + K M + V+GK   G+
Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGKLPFGV 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  +PKG ++D AV  WK L +D  A FDTVV L A +I PQV+WGT+P  V+
Sbjct: 244 TVEYVKGRPFSPKGAEWDMAVEAWKDLVSDADAKFDTVVELDATQIKPQVSWGTSPEMVL 303

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

Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           A IAKGRKVA  + QA+VVPGSG VKAQAEAEGLDKIF+EAGFEWR PGCSMCLAMN DR
Sbjct: 364 AVIAKGRKVASTIKQAIVVPGSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDR 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: 743
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 AO356_21400 AO356_21400 (isopropylmalate isomerase)
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.2682.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.5e-238  776.0   1.6   6.8e-238  775.7   1.6    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400  AO356_21400 isopropylmalate isom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400  AO356_21400 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  775.7   1.6  6.8e-238  6.8e-238       2     466 .]       3     471 ..       2     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 775.7 bits;  conditional E-value: 6.8e-238
                                       TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhn 64 
                                                      ktly+kl+d+h+vk+ ++++ l+yidrh++hevtspqafeglr agrk  r+d  +at dhn
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400   3 GKTLYDKLWDSHLVKQRDDGSALIYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPDHN 65 
                                                     59************************************************************* PP

                                       TIGR00170  65 istesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgkt 123
                                                     ++t+         i +++++lqv++l+ n++e+g+  f +++++qgivhv+gpe+g tlpg+t
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400  66 VPTTPErkggIEAIADQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGATLPGMT 128
                                                     **9865466334578999********************************************* PP

                                       TIGR00170 124 ivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiila 186
                                                     +vcgdsht+thgafgala gigtsevehvlatq l+ ++ k++ ++vegkl  g+takdi+la
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 129 VVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGKLPFGVTAKDIVLA 191
                                                     *************************************************************** PP

                                       TIGR00170 187 iigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkya 249
                                                     +igkig+agg g+ +efag airdls+e+rmt+cnm+ieaga+ gl+a de t eyvk+r+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 192 VIGKIGTAGGNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADEKTVEYVKGRPFS 254
                                                     *************************************************************** PP

                                       TIGR00170 250 pkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpkslad 312
                                                     pkg+e++ av+ wk l +d +akfd+vv l+a++i pqv+wgt+p++vl+v+++vpdp++  d
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 255 PKGAEWDMAVEAWKDLVSDADAKFDTVVELDATQIKPQVSWGTSPEMVLAVDQNVPDPAKEMD 317
                                                     *************************************************************** PP

                                       TIGR00170 313 pvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklal 375
                                                      v++ s+ +al+y+gl +++ ++di++d+vfigsctnsriedlraaa ++kg+kva+++k+a+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 318 LVKRDSIVRALKYMGLSANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAI 380
                                                     *************************************************************** PP

                                       TIGR00170 376 vvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                                     vvpgsglvk+qae+egldkifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 381 VVPGSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQG 443
                                                     *************************************************************** PP

                                       TIGR00170 439 kgarthlvspamaaaaavagkfvdirel 466
                                                     +g+rthlvspamaaaaav+g+fvd+rel
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21400 444 AGGRTHLVSPAMAAAAAVNGRFVDVREL 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: 00:00:00.02
# Mc/sec: 7.50
//
[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