GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Phaeobacter inhibens BS107

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate GFF2640 PGA1_c26800 phenylacetate-CoA ligase PaaK

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__Phaeo:GFF2640
          Length = 436

 Score =  604 bits (1557), Expect = e-177
 Identities = 299/436 (68%), Positives = 350/436 (80%), Gaps = 4/436 (0%)

Query: 5   TPSPGDLEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADL 64
           +P  G+L+PIE AS DE+R+LQL+RLKWS+RHAY+NV  Y++ FD  GVHPDDL+ L+DL
Sbjct: 5   SPKKGELDPIEIASIDEIRSLQLDRLKWSLRHAYDNVAMYKQRFDEAGVHPDDLQQLSDL 64

Query: 65  AKFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARS 124
           AKFPFT K DLRDNYPFG+FAVPRE++ R+HASSGTTGKPTVVGYT  DI  WA +VARS
Sbjct: 65  AKFPFTYKNDLRDNYPFGLFAVPREQIMRLHASSGTTGKPTVVGYTANDISNWADLVARS 124

Query: 125 IRASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDI 184
           +RASG R GDMVH AYGYGLFTGGLGAHYG E+LG TVVPMSGGQTEKQ+ LI DFKPD 
Sbjct: 125 LRASGLRKGDMVHNAYGYGLFTGGLGAHYGIERLGATVVPMSGGQTEKQVGLITDFKPDG 184

Query: 185 IMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLS 244
           IMVTPSYML +L++  ++G+DP + SLKVG+FGAEPWT AMR  +E    + AVDIYGLS
Sbjct: 185 IMVTPSYMLNILEQYHKVGMDPRECSLKVGVFGAEPWTDAMRREVEQAFDMHAVDIYGLS 244

Query: 245 EVMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIR 304
           E+MGPGVANEC+E KDGPVIWEDHF PEIIDP TGEVLPDG  GELVFTTLTKE +P++R
Sbjct: 245 EIMGPGVANECVETKDGPVIWEDHFLPEIIDPQTGEVLPDGEMGELVFTTLTKEGLPMVR 304

Query: 305 YRTRDLTRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLE 364
           YRTRDLTRLLP TARSMRRM KITGRSDDM+I+RGVN+FP+QVEE +     LAP Y +E
Sbjct: 305 YRTRDLTRLLPGTARSMRRMEKITGRSDDMIILRGVNVFPSQVEEQLLATGGLAPYYQIE 364

Query: 365 VDKDGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIER 424
           + K G MD + V VE NP+A        K A A+ L   IK  +GVS ++ V EP ++ER
Sbjct: 365 LYKSGRMDAMRVFVEANPDAT---DELSKTAAARMLTKRIKDMVGVSTEIIVGEPGSVER 421

Query: 425 VTIGKAKRVVDRRPKE 440
            + GKAKRVVD R KE
Sbjct: 422 -SQGKAKRVVDNRSKE 436


Lambda     K      H
   0.318    0.137    0.406 

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: 668
Number of extensions: 16
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: 440
Length of database: 436
Length adjustment: 32
Effective length of query: 408
Effective length of database: 404
Effective search space:   164832
Effective search space used:   164832
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF2640 PGA1_c26800 (phenylacetate-CoA ligase PaaK)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

# 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/TIGR02155.hmm
# target sequence database:        /tmp/gapView.898494.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02155  [M=422]
Accession:   TIGR02155
Description: PA_CoA_ligase: phenylacetate-CoA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-219  714.4   0.0     2e-219  714.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2640  PGA1_c26800 phenylacetate-CoA li


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2640  PGA1_c26800 phenylacetate-CoA ligase PaaK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.3   0.0    2e-219    2e-219       1     422 []      15     433 ..      15     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 714.3 bits;  conditional E-value: 2e-219
                          TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavprek 76 
                                        e +s de+r+lql+rlk+s+++ay+nv++y+++fd+agv+pddl++lsdlakfp+t k+dlrdnypf+l+avpre+
  lcl|FitnessBrowser__Phaeo:GFF2640  15 EIASIDEIRSLQLDRLKWSLRHAYDNVAMYKQRFDEAGVHPDDLQQLSDLAKFPFTYKNDLRDNYPFGLFAVPREQ 90 
                                        6799************************************************************************ PP

                          TIGR02155  77 vvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpis 152
                                        ++r+hassGttGkptvv+yt++d+ +w+++varslra+G rkgd++hnayGyGlftGGlG+hyG e+lGatvvp+s
  lcl|FitnessBrowser__Phaeo:GFF2640  91 IMRLHASSGTTGKPTVVGYTANDISNWADLVARSLRASGLRKGDMVHNAYGYGLFTGGLGAHYGIERLGATVVPMS 166
                                        **************************************************************************** PP

                          TIGR02155 153 GGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikaldiyG 228
                                        GGqtekqv li dfkpd i+vtpsy+l++le+ +++g+dp+++slkv+++Gaepwt+amr+e+e++++++a+diyG
  lcl|FitnessBrowser__Phaeo:GFF2640 167 GGQTEKQVGLITDFKPDGIMVTPSYMLNILEQYHKVGMDPRECSLKVGVFGAEPWTDAMRREVEQAFDMHAVDIYG 242
                                        **************************************************************************** PP

                          TIGR02155 229 lseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrllpgta 304
                                        lse++GpGvanecvetkdG+viwedhf peiidp+tgevlpdGe Gelvfttltke+lp++ryrtrdltrllpgta
  lcl|FitnessBrowser__Phaeo:GFF2640 243 LSEIMGPGVANECVETKDGPVIWEDHFLPEIIDPQTGEVLPDGEMGELVFTTLTKEGLPMVRYRTRDLTRLLPGTA 318
                                        **************************************************************************** PP

                          TIGR02155 305 rtmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqks 380
                                        r+mrrm+ki+Grsdd++ilrGvnvfp+q+ee ll+++ l+p yq+el ++G++d + + ve+++++++     +k+
  lcl|FitnessBrowser__Phaeo:GFF2640 319 RSMRRMEKITGRSDDMIILRGVNVFPSQVEEQLLATGGLAPYYQIELYKSGRMDAMRVFVEANPDATDEL---SKT 391
                                        ***************************************************************9998877...455 PP

                          TIGR02155 381 llakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                        + a+ + k+ik++vgvs+++ + epgs+ers+Gkakrvvd+r
  lcl|FitnessBrowser__Phaeo:GFF2640 392 AAARMLTKRIKDMVGVSTEIIVGEPGSVERSQGKAKRVVDNR 433
                                        66999***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (436 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.34
//
[ok]

This GapMind analysis is from Sep 17 2021. 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