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 GFF2655 HP15_2599 isopropylmalate isomerase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Marino:GFF2655
          Length = 469

 Score =  546 bits (1406), Expect = e-160
 Identities = 276/469 (58%), Positives = 347/469 (73%), Gaps = 7/469 (1%)

Query: 2   AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGR-PVRQPGKTFAT 60
           A+TLY+KL+  H+V E  + + LLYIDRHL+HEVT+PQAF GLR+ GR P R P    A 
Sbjct: 3   ARTLYDKLWQRHLVDELPDGSALLYIDRHLLHEVTTPQAFSGLRSAGRKPWRIPANV-AV 61

Query: 61  MDHNVSTQTKDINACG---EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGV 117
            DH V T+ +++   G    +AR Q++ L +NC+EFG+ L +L    QGIVHV+GPEQG+
Sbjct: 62  PDHAVPTRKRELGVAGIADRVARKQVETLSRNCEEFGIPLIELEDARQGIVHVVGPEQGL 121

Query: 118 TLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPG 177
           TLPGMTIVCGDSHT+THGAF  LA GIGTSEVEHVLATQTL+  + K M++  +G+   G
Sbjct: 122 TLPGMTIVCGDSHTSTHGAFATLAMGIGTSEVEHVLATQTLRTQKQKNMRVVFEGQPGFG 181

Query: 178 ITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDE 237
           +T KD++LA+IG+ G+AGG G+ +E+ G AIR+LSMEGRMT+CNM+IE GA+AG+VA D 
Sbjct: 182 VTPKDLILALIGRIGTAGGNGYAIEYAGAAIRNLSMEGRMTICNMSIEAGARAGMVAYDR 241

Query: 238 TTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQV 297
            T  YV+GR  AP G+  + A  YW+TL +D  A FD       E + PQVTWGT+P  V
Sbjct: 242 VTEQYVEGRPQAPVGERLEQAREYWRTLVSDAEADFDREEHFPLEALVPQVTWGTSPEMV 301

Query: 298 ISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRA 357
             ++   PD +  A P +R SA +AL YMGL+PG PL  ++IDKVFIGSCTN+R+EDLRA
Sbjct: 302 TGIDGKTPDLSQLA-PEKRESARRALDYMGLEPGRPLKGLSIDKVFIGSCTNARMEDLRA 360

Query: 358 AAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNND 416
            A + +G+KV   V QAL+VPGSG V+ QAE EGLD IF  AGFEWR  GCSMCL MN+D
Sbjct: 361 VANLVQGQKVHRSVKQALIVPGSGQVRLQAEREGLDMIFRNAGFEWRAAGCSMCLGMNDD 420

Query: 417 RLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           RLNPGERCASTSNRNFEGRQG+GGRTHL+SP MAAAAA+ G   D+R +
Sbjct: 421 RLNPGERCASTSNRNFEGRQGKGGRTHLMSPLMAAAAALAGEITDVREV 469


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: 707
Number of extensions: 27
Number of successful extensions: 4
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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 GFF2655 HP15_2599 (isopropylmalate isomerase 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.445.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-215  701.7   0.0   2.4e-215  701.4   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2655  HP15_2599 isopropylmalate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2655  HP15_2599 isopropylmalate isomerase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  701.4   0.0  2.4e-215  2.4e-215       2     466 .]       3     469 .]       2     469 .] 0.98

  Alignments for each domain:
  == domain 1  score: 701.4 bits;  conditional E-value: 2.4e-215
                           TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdv...e 73 
                                         a+tly+kl++ h+v e  +++ llyidrhl+hevt+pqaf glr+agrk  r+   +a  dh+++t++r++    
  lcl|FitnessBrowser__Marino:GFF2655   3 ARTLYDKLWQRHLVDELPDGSALLYIDRHLLHEVTTPQAFSGLRSAGRKPWRIPANVAVPDHAVPTRKRELgvaG 77 
                                         89*******************************************************************752225 PP

                           TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtse 148
                                         i + +a+ qv++l++n++efg++l++l++a+qgivhvvgpe+gltlpg+tivcgdsht+thgaf +la+gigtse
  lcl|FitnessBrowser__Marino:GFF2655  78 IADRVARKQVETLSRNCEEFGIPLIELEDARQGIVHVVGPEQGLTLPGMTIVCGDSHTSTHGAFATLAMGIGTSE 152
                                         7899*********************************************************************** PP

                           TIGR00170 149 vehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnma 223
                                         vehvlatqtl+ ++ k++++  eg+   g+t kd+ila+ig+ig+agg gy +e+ag air+lsme+rmt+cnm+
  lcl|FitnessBrowser__Marino:GFF2655 153 VEHVLATQTLRTQKQKNMRVVFEGQPGFGVTPKDLILALIGRIGTAGGNGYAIEYAGAAIRNLSMEGRMTICNMS 227
                                         *************************************************************************** PP

                           TIGR00170 224 ieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvl 298
                                         ieaga+ag++a d +t +yv +r++ap g+  e+a +yw+tl +d +a fd++  +  + ++pqvtwgt+p++v 
  lcl|FitnessBrowser__Marino:GFF2655 228 IEAGARAGMVAYDRVTEQYVEGRPQAPVGERLEQAREYWRTLVSDAEADFDREEHFPLEALVPQVTWGTSPEMVT 302
                                         *************************************************************************** PP

                           TIGR00170 299 svneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvkl 373
                                          ++++ pd  +la p +++sa +al+y+glepg +lk + +dkvfigsctn+r+edlra a++v+g+kv  +vk+
  lcl|FitnessBrowser__Marino:GFF2655 303 GIDGKTPDLSQLA-PEKRESARRALDYMGLEPGRPLKGLSIDKVFIGSCTNARMEDLRAVANLVQGQKVHRSVKQ 376
                                         ********99996.7799********************************************************* PP

                           TIGR00170 374 alvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvsp 448
                                         al+vpgsg+v+ qae+egld if +agfewr agcs+clgmn+d+l+++ercastsnrnfegrqgkg+rthl+sp
  lcl|FitnessBrowser__Marino:GFF2655 377 ALIVPGSGQVRLQAEREGLDMIFRNAGFEWRAAGCSMCLGMNDDRLNPGERCASTSNRNFEGRQGKGGRTHLMSP 451
                                         *************************************************************************** PP

                           TIGR00170 449 amaaaaavagkfvdirel 466
                                          maaaaa+ag++ d+re+
  lcl|FitnessBrowser__Marino:GFF2655 452 LMAAAAALAGEITDVREV 469
                                         ****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (469 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: 9.84
//
[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