Alignments for a candidate for leuC in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF1877 HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region domain

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Marino:GFF1877
          Length = 472

 Score =  597 bits (1540), Expect = e-175
 Identities = 295/467 (63%), Positives = 358/467 (76%), Gaps = 4/467 (0%)

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

Query: 63  HNVSTQTKDINACG---EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HNV T  +D    G    ++RIQ++ L KNC EFG+  + +    QGIVHV+GPEQG TL
Sbjct: 64  HNVPTTDRDRGVEGIVDPVSRIQVETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATL 123

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGM+IVCGDSHT+THGAFG LA GIGTSEVEHVLATQ L Q + K M ++V GK  PG+T
Sbjct: 124 PGMSIVCGDSHTSTHGAFGCLAHGIGTSEVEHVLATQCLVQQKMKNMLVKVNGKLGPGVT 183

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD+VLAIIGK G+AGGTGH +EF GEAIR LSMEGRMT+CNM+IE GA+ G+VA D+TT
Sbjct: 184 GKDVVLAIIGKIGTAGGTGHAIEFGGEAIRGLSMEGRMTICNMSIEAGARVGMVAVDDTT 243

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
             YV+ R   PKG+ +D AV YW+TL +D  A FD +V L+  EI PQV+WGT+P  V  
Sbjct: 244 IEYVRNRPFGPKGEQWDAAVEYWRTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVAG 303

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           ++  +PDP   ADP++R    +AL YMGL+P + +T++ +D+VFIGSCTNSRIEDLR AA
Sbjct: 304 IDGKVPDPEQEADPIKREGIVRALKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAA 363

Query: 360 EIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
            + KGRKV+P + QA+VVPGSG VKAQAE EGLDKIFIEAG EWR PGCSMCLAMN D+L
Sbjct: 364 AVVKGRKVSPILKQAMVVPGSGLVKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKL 423

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
             GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAVTGHF D+R +
Sbjct: 424 GQGEHCASTSNRNFEGRQGFGGRTHLVSPAMAAAAAVTGHFVDVREL 470


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: 759
Number of extensions: 24
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 GFF1877 HP15_1834 (protein containing 3-isopropylmalate dehydratase, large subunit region domain)
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.29552.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-239  781.3   0.4   1.7e-239  781.0   0.4    1.0  1  lcl|FitnessBrowser__Marino:GFF1877  HP15_1834 protein containing 3-i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1877  HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  781.0   0.4  1.7e-239  1.7e-239       2     466 .]       3     470 ..       2     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 781.0 bits;  conditional E-value: 1.7e-239
                           TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve... 73 
                                          ktly+kl+d h+vk+ ++++ l+yidr l+hevtspqafeglr agrk  r+d  +at dhn++t+ rd     
  lcl|FitnessBrowser__Marino:GFF1877   3 GKTLYDKLWDDHLVKQRDDGSALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRIDANIATPDHNVPTTDRDRGveg 77 
                                         59*******************************************************************854113 PP

                           TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtse 148
                                         i++ ++++qv++l+kn++efg+  f +++++qgivhv+gpe+g tlpg++ivcgdsht+thgafg+la gigtse
  lcl|FitnessBrowser__Marino:GFF1877  78 IVDPVSRIQVETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATLPGMSIVCGDSHTSTHGAFGCLAHGIGTSE 152
                                         7899*********************************************************************** PP

                           TIGR00170 149 vehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnma 223
                                         vehvlatq l+q++ k++ ++v+gkl +g+t kd++laiigkig+aggtg+ +ef geair lsme+rmt+cnm+
  lcl|FitnessBrowser__Marino:GFF1877 153 VEHVLATQCLVQQKMKNMLVKVNGKLGPGVTGKDVVLAIIGKIGTAGGTGHAIEFGGEAIRGLSMEGRMTICNMS 227
                                         *************************************************************************** PP

                           TIGR00170 224 ieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvl 298
                                         ieaga+ g++a d+tt+eyv++r++ pkg++++ av+yw+tl++d +a+fdk v le+++i pqv+wgt+p++v 
  lcl|FitnessBrowser__Marino:GFF1877 228 IEAGARVGMVAVDDTTIEYVRNRPFGPKGEQWDAAVEYWRTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVA 302
                                         *************************************************************************** PP

                           TIGR00170 299 svneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvkl 373
                                          ++++vpdp++ adp++++++ +al+y+gl+p++ ++dik+d+vfigsctnsriedlr+aa+vvkg+kv++ +k+
  lcl|FitnessBrowser__Marino:GFF1877 303 GIDGKVPDPEQEADPIKREGIVRALKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAAAVVKGRKVSPILKQ 377
                                         *************************************************************************** PP

                           TIGR00170 374 alvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvsp 448
                                         a+vvpgsglvk+qae+egldkif+eag+ewr++gcs+cl+mn d+l+++e castsnrnfegrqg g+rthlvsp
  lcl|FitnessBrowser__Marino:GFF1877 378 AMVVPGSGLVKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKLGQGEHCASTSNRNFEGRQGFGGRTHLVSP 452
                                         *************************************************************************** PP

                           TIGR00170 449 amaaaaavagkfvdirel 466
                                         amaaaaav+g+fvd+rel
  lcl|FitnessBrowser__Marino:GFF1877 453 AMAAAAAVTGHFVDVREL 470
                                         ****************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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.01
//
[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