Alignments for a candidate for leuC in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Pseudomonas simiae WCS417

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF3634 PS417_18600 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__WCS417:GFF3634
          Length = 472

 Score =  591 bits (1524), Expect = e-173
 Identities = 299/468 (63%), Positives = 360/468 (76%), Gaps = 5/468 (1%)

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

Query: 63  HNVSTQTK---DINACGE-MARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
           HNV T  +    I+A  + ++R+Q+Q L   C E+G+  + +N   QGIVHV+GPEQG T
Sbjct: 64  HNVPTTPERKGGIDAIADQVSRLQVQTLDDYCDEYGITEFKMNDVRQGIVHVIGPEQGAT 123

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMT+VCGDSHT+THGAFGALA GIGTSEVEHV ATQ L   + K M ++V+G    G+
Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVFATQCLVAKKMKNMLVKVEGTLPFGV 183

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

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
           T  YVKGR  AP+G D+D AV  WK L +D  A FDTVV L A +I PQV+WGT+P  V+
Sbjct: 244 TVEYVKGRPFAPQGADWDAAVEAWKDLVSDADAVFDTVVELDAAQIKPQVSWGTSPEMVL 303

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
           +V+ N+PDPA   D V+R S E+AL YMGL+    +T++ +D+VFIGSCTNSRIEDLRAA
Sbjct: 304 AVDQNVPDPAKETDLVKRGSIERALKYMGLQANQAITDIQLDRVFIGSCTNSRIEDLRAA 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 LESGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVNGRFIDVREL 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: 732
Number of extensions: 21
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 GFF3634 PS417_18600 (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.14181.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.5e-236  768.7   1.6   1.2e-235  768.4   1.6    1.0  1  lcl|FitnessBrowser__WCS417:GFF3634  PS417_18600 isopropylmalate isom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3634  PS417_18600 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.4   1.6  1.2e-235  1.2e-235       2     466 .]       3     471 ..       2     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 768.4 bits;  conditional E-value: 1.2e-235
                           TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr....dv 72 
                                          ktly+kl+d+h vk+ +++++l+yidrh++hevtspqafeglr agrk  rvd+ +at dhn++t+        
  lcl|FitnessBrowser__WCS417:GFF3634   3 GKTLYDKLWDSHEVKRRDDGSSLIYIDRHIIHEVTSPQAFEGLRLAGRKPWRVDSIIATPDHNVPTTPErkggID 77 
                                         59***************************************************************9865467423 PP

                           TIGR00170  73 eikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147
                                          i +++++lqv++l+  ++e+g+  f +++++qgivhv+gpe+g tlpg+t+vcgdsht+thgafgala gigts
  lcl|FitnessBrowser__WCS417:GFF3634  78 AIADQVSRLQVQTLDDYCDEYGITEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGTS 152
                                         578999********************************************************************* PP

                           TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnm 222
                                         evehv+atq l+ ++ k++ ++veg+l  g+takdi+la+igkig+agg g+ +efag airdls+e+rmt+cnm
  lcl|FitnessBrowser__WCS417:GFF3634 153 EVEHVFATQCLVAKKMKNMLVKVEGTLPFGVTAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRDLSIEGRMTICNM 227
                                         *************************************************************************** PP

                           TIGR00170 223 aieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqv 297
                                         +ieaga+ g++a de t eyvk+r++ap+g++++ av+ wk l +d +a+fd+vv l+a +i pqv+wgt+p++v
  lcl|FitnessBrowser__WCS417:GFF3634 228 SIEAGARVGMVAADEKTVEYVKGRPFAPQGADWDAAVEAWKDLVSDADAVFDTVVELDAAQIKPQVSWGTSPEMV 302
                                         *************************************************************************** PP

                           TIGR00170 298 lsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvk 372
                                         l+v+++vpdp++ +d v++ s+e+al+y+gl++++ ++di++d+vfigsctnsriedlraaa ++kg+kva+++k
  lcl|FitnessBrowser__WCS417:GFF3634 303 LAVDQNVPDPAKETDLVKRGSIERALKYMGLQANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIK 377
                                         *************************************************************************** PP

                           TIGR00170 373 lalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvs 447
                                         +a+vvpgsglvk+qae+egldkifleagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg+g+rthlvs
  lcl|FitnessBrowser__WCS417:GFF3634 378 QAIVVPGSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQGAGGRTHLVS 452
                                         *************************************************************************** PP

                           TIGR00170 448 pamaaaaavagkfvdirel 466
                                         pamaaaaav+g+f+d+rel
  lcl|FitnessBrowser__WCS417:GFF3634 453 PAMAAAAAVNGRFIDVREL 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: 11.89
//
[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