Alignments for a candidate for hcs in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Polaromonas naphthalenivorans CJ2

Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate WP_011801696.1 PNAP_RS11555 homocitrate synthase

Query= SwissProt::P05342
         (385 letters)



>NCBI__GCF_000015505.1:WP_011801696.1
          Length = 395

 Score =  381 bits (978), Expect = e-110
 Identities = 199/368 (54%), Positives = 260/368 (70%), Gaps = 2/368 (0%)

Query: 3   SVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAIAG 62
           ++II+DTTLRDGEQ+AGVAF  DEK AIA ALA  GVPE+EIGIP+MGEEE + ++ IA 
Sbjct: 4   NLIINDTTLRDGEQTAGVAFTVDEKCAIACALAAAGVPEMEIGIPAMGEEEIDCINTIAA 63

Query: 63  LGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARLVG 122
           L L + L+ W RL D DLA+A      ++ LS+PVSD+ L HKL + R+W L +V R++ 
Sbjct: 64  LELPAALMIWGRLTDADLASALRCQADIIHLSIPVSDIHLRHKLRQSREWVLAQVTRVIE 123

Query: 123 EARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFRFL 182
           +A  +G ++ LG EDASRAD  F+ QV   AQ  GA R+RFADT+GV++PF   +    L
Sbjct: 124 KAVASGRKISLGAEDASRADAGFLSQVARRAQDCGASRIRFADTLGVLDPFTTYEAITRL 183

Query: 183 SRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALKNL 242
              + +++E+HAH+D GLATANTLAA+  GATH NTTVNGLGERAGNAALEE V+ +++L
Sbjct: 184 REAVHLDIEIHAHNDLGLATANTLAALRAGATHANTTVNGLGERAGNAALEEVVMGVRHL 243

Query: 243 HGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYEGL 302
           H   TG+ T+ + +IS LV RASGRQVA+ KS+VG  VFTHE+GIH+DGLLK+   YE  
Sbjct: 244 HHAQTGVSTQALVSISRLVARASGRQVAFNKSIVGEAVFTHESGIHIDGLLKNASTYESF 303

Query: 303 NPDELGRSHSLVLGKHSGAHMVRNTYRDLGIEL-ADWQSQALLGRIRAFSTRTKRRSPQP 361
           +P ELGR    VLGKHSG+  VR  Y  +G+ L  D  +  +L RIR  + R K+ +  P
Sbjct: 304 DPSELGRERRTVLGKHSGSQSVRQAYGAMGVVLDDDALTGRVLARIRDHAMRVKQEA-TP 362

Query: 362 AELQDFYR 369
            EL+ F R
Sbjct: 363 DELRGFLR 370


Lambda     K      H
   0.320    0.135    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: 475
Number of extensions: 15
Number of successful extensions: 1
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: 385
Length of database: 395
Length adjustment: 31
Effective length of query: 354
Effective length of database: 364
Effective search space:   128856
Effective search space used:   128856
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_011801696.1 PNAP_RS11555 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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/TIGR02660.hmm
# target sequence database:        /tmp/gapView.3101.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.2e-157  507.9   9.2     1e-156  507.7   9.2    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011801696.1  PNAP_RS11555 homocitrate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011801696.1  PNAP_RS11555 homocitrate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.7   9.2    1e-156    1e-156       2     363 ..       5     367 ..       4     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 507.7 bits;  conditional E-value: 1e-156
                                 TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 
                                               ++inDttLRDGEq+agvaF+ +EK+aiA aL++aGv+e+E+GipamgeeE++ i++iaal+l+a+l+ W
  lcl|NCBI__GCF_000015505.1:WP_011801696.1   5 LIINDTTLRDGEQTAGVAFTVDEKCAIACALAAAGVPEMEIGIPAMGEEEIDCINTIAALELPAALMIW 73 
                                               79******************************************************************* PP

                                 TIGR02660  71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139
                                                Rl+++d+++a ++  + ++ls+pvsd++l++kl+++r+wvl+++++++++a  +g k+s+gaeDasRa
  lcl|NCBI__GCF_000015505.1:WP_011801696.1  74 GRLTDADLASALRCQADIIHLSIPVSDIHLRHKLRQSREWVLAQVTRVIEKAVASGRKISLGAEDASRA 142
                                               ********************************************************************* PP

                                 TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208
                                               d+ fl ++a+ a++ ga+R+RfaDt+gvldPf+tye++++lr+a++l++E+HaHnDlGlAtAntlaa++
  lcl|NCBI__GCF_000015505.1:WP_011801696.1 143 DAGFLSQVARRAQDCGASRIRFADTLGVLDPFTTYEAITRLREAVHLDIEIHAHNDLGLATANTLAALR 211
                                               ********************************************************************* PP

                                 TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277
                                               aGa+++++tv+GlGERAGnAaleev++++++l++ +tg+++++l ++s+lva+asgr+++ +k++vGe+
  lcl|NCBI__GCF_000015505.1:WP_011801696.1 212 AGATHANTTVNGLGERAGNAALEEVVMGVRHLHHAQTGVSTQALVSISRLVARASGRQVAFNKSIVGEA 280
                                               ********************************************************************* PP

                                 TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeee.aeelleav 345
                                               vF+HEsGiH+dgllk+++tYes+dP+e+Grer+ v+GKHsg+++v++a+ ++g+ l+++  + ++l+++
  lcl|NCBI__GCF_000015505.1:WP_011801696.1 281 VFTHESGIHIDGLLKNASTYESFDPSELGRERRTVLGKHSGSQSVRQAYGAMGVVLDDDAlTGRVLARI 349
                                               ********************************************************98761579***** PP

                                 TIGR02660 346 ravaerlKrsleeeelaa 363
                                               r++a r+K+ ++ +el+ 
  lcl|NCBI__GCF_000015505.1:WP_011801696.1 350 RDHAMRVKQEATPDELRG 367
                                               **************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (395 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: 8.42
//
[ok]

This GapMind analysis is from Apr 10 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