GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Desulfoscipio geothermicus DSM 3669

Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_092482666.1 BM299_RS06535 lysine 2,3-aminomutase

Query= SwissProt::Q9XBQ8
         (416 letters)



>NCBI__GCF_900115975.1:WP_092482666.1
          Length = 414

 Score =  545 bits (1404), Expect = e-159
 Identities = 251/399 (62%), Positives = 318/399 (79%)

Query: 5   RYELFKDVSDADWNDWRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSLRMAITPYYL 64
           R   ++DV  +DWNDWRWQ+RNRI +V++L++ + +  EE   +++C+K  RMAITPYY 
Sbjct: 7   RVPYYQDVPASDWNDWRWQIRNRITSVDKLREVLGIQDEEAGEISRCLKHFRMAITPYYA 66

Query: 65  SLIDPNDPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDM 124
           SLID ++ + P+++QA+PT  ELN   AD+ DPLHED DSPVPG+THRYPDRVLLL+TD 
Sbjct: 67  SLIDSSNKDCPIKRQAVPTIDELNFEEADMSDPLHEDVDSPVPGITHRYPDRVLLLVTDQ 126

Query: 125 CSMYCRHCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYI 184
           CSMYCRHCTRRR AG  D ++P  ++D+AI YI+N  +VRDVL+SGGD L +SDE LEYI
Sbjct: 127 CSMYCRHCTRRRMAGGKDRALPRAQVDRAIAYIQNNKKVRDVLISGGDPLTLSDEHLEYI 186

Query: 185 IAKLREIPHVEIVRIGSRTPVVLPQRITPELVNMLKKYHPVWLNTHFNHPNEITEESTRA 244
           I +LR + HVEI+RIG+RTPVVLPQRITPEL  ML+KYHPVW+NTHFNHP EIT  S  +
Sbjct: 187 IRRLRAVKHVEIIRIGTRTPVVLPQRITPELCAMLQKYHPVWINTHFNHPAEITLASKAS 246

Query: 245 CQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTP 304
           C+ LADAG+PLGNQSVLLRG+NDC ++MK+L+++L+ +RVRPYY+YQCDLS G+ HFRT 
Sbjct: 247 CERLADAGIPLGNQSVLLRGINDCTNIMKKLLHQLMMMRVRPYYLYQCDLSRGIGHFRTS 306

Query: 305 VSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKTPVMPNYVISQSHDKVILRNFEGVITT 364
           V KGIEI+E LRGHT+G  VPT+VVDAPGGGGK PVMP Y IS+S +KVILRNFEG + +
Sbjct: 307 VGKGIEIMENLRGHTTGLAVPTYVVDAPGGGGKIPVMPQYAISRSDNKVILRNFEGNVYS 366

Query: 365 YSEPINYTPGCNCDVCTGKKKVHKVGVAGLLNGEGMALE 403
           Y+EP  Y   C+C+ C  KK  +  G AGL+ G  +ALE
Sbjct: 367 YTEPAGYDADCHCEDCNNKKGKNSPGPAGLMKGNEVALE 405


Lambda     K      H
   0.320    0.138    0.422 

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: 582
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: 416
Length of database: 414
Length adjustment: 31
Effective length of query: 385
Effective length of database: 383
Effective search space:   147455
Effective search space used:   147455
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_092482666.1 BM299_RS06535 (lysine 2,3-aminomutase)
to HMM TIGR03820 (ablA: lysine-2,3-aminomutase (EC 5.4.3.2))

# 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.carbon/TIGR03820.hmm
# target sequence database:        /tmp/gapView.291660.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03820  [M=417]
Accession:   TIGR03820
Description: lys_2_3_AblA: lysine-2,3-aminomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-189  616.5   0.1   1.2e-189  616.2   0.1    1.0  1  NCBI__GCF_900115975.1:WP_092482666.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900115975.1:WP_092482666.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.2   0.1  1.2e-189  1.2e-189       4     380 ..      16     386 ..      13     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 616.2 bits;  conditional E-value: 1.2e-189
                             TIGR03820   4 eeewkdwkwqlrnsikdvdtlekllgiklseeekeelketvekfplsitpyylslidaedlendpiflqsvps 76 
                                           +++w+dw+wq+rn+i++vd+l+++lgi  ++ee  e+ + +++f ++itpyy+slid+++  + pi +q+vp+
  NCBI__GCF_900115975.1:WP_092482666.1  16 ASDWNDWRWQIRNRITSVDKLREVLGI--QDEEAGEISRCLKHFRMAITPYYASLIDSSNKDC-PIKRQAVPT 85 
                                           689*********************998..588999*************************999.********* PP

                             TIGR03820  77 skelevesadledplaedkdspvegithrypdrvlflvsntcamycrhctrkrkvgdkdsipskeeikegiey 149
                                           ++el++e+ad++dpl+ed dspv+githrypdrvl+lv+++c+mycrhctr+r +g kd +  + +++++i y
  NCBI__GCF_900115975.1:WP_092482666.1  86 IDELNFEEADMSDPLHEDVDSPVPGITHRYPDRVLLLVTDQCSMYCRHCTRRRMAGGKDRALPRAQVDRAIAY 158
                                           ************************************************************************* PP

                             TIGR03820 150 iretpqvrdvllsGGdplllsdelldwilselkaiehveviriGtrvpvvlpyritdelveilkkyhpvwlnt 222
                                           i+++++vrdvl+sGGdpl lsde l++i+  l+a++hve+iriGtr+pvvlp+rit+el+++l+kyhpvw+nt
  NCBI__GCF_900115975.1:WP_092482666.1 159 IQNNKKVRDVLISGGDPLTLSDEHLEYIIRRLRAVKHVEIIRIGTRTPVVLPQRITPELCAMLQKYHPVWINT 231
                                           ************************************************************************* PP

                             TIGR03820 223 hfnhpkeitksskkalakladaGiplGnqsvllagvndcprilkklvhklvknrvrpyylyqcdlseGlshfr 295
                                           hfnhp eit  sk+++++ladaGiplGnqsvll+g+ndc++i+kkl h+l+  rvrpyylyqcdls+G+ hfr
  NCBI__GCF_900115975.1:WP_092482666.1 232 HFNHPAEITLASKASCERLADAGIPLGNQSVLLRGINDCTNIMKKLLHQLMMMRVRPYYLYQCDLSRGIGHFR 304
                                           ************************************************************************* PP

                             TIGR03820 296 tpvskGieilesliGhtsGfavptyvvdapgGGGkipvmpnylisqstnkvvlrnyeGvittykepdsyeeal 368
                                           t+v+kGiei+e+l+Ght+G+avptyvvdapgGGGkipvmp+y is s+nkv+lrn+eG + +y+ep+ y++  
  NCBI__GCF_900115975.1:WP_092482666.1 305 TSVGKGIEIMENLRGHTTGLAVPTYVVDAPGGGGKIPVMPQYAISRSDNKVILRNFEGNVYSYTEPAGYDA-- 375
                                           **********************************************************************9.. PP

                             TIGR03820 369 cdrkcekcelkl 380
                                            d +ce+c++k 
  NCBI__GCF_900115975.1:WP_092482666.1 376 -DCHCEDCNNKK 386
                                           .55677777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (414 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: 00:00:00.00
# Mc/sec: 21.48
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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