GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Pseudarthrobacter sulfonivorans Ar51

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_058931420.1 AU252_RS15070 phenylacetate--CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>NCBI__GCF_001484605.1:WP_058931420.1
          Length = 454

 Score =  511 bits (1316), Expect = e-149
 Identities = 268/450 (59%), Positives = 325/450 (72%), Gaps = 17/450 (3%)

Query: 2   PVKTPSPGDLEPI----EKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDD 57
           P+  P+    +PI    E  S+DEL ALQL RL+ +V +AY+ VP Y++ FD  G+HP D
Sbjct: 9   PMPQPTSQGTDPILDREETISRDELEALQLTRLQHTVAYAYDRVPLYKRKFDDAGIHPTD 68

Query: 58  LKSLADLAKFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTW 117
           L+ L+DL  FPFT K DLR  YPFGMFAVP+ +VARVHASSGTTG+PTVVGYT +D+  W
Sbjct: 69  LRELSDLGNFPFTTKEDLRAEYPFGMFAVPQSEVARVHASSGTTGRPTVVGYTKQDLADW 128

Query: 118 ATVVARSIRASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLI 177
           A +VAR +RASG R G  VH AYGYGLFTGGLGAH GAE LGCTV+PMSGGQTE+QIQLI
Sbjct: 129 AKLVARCLRASGVRPGMKVHNAYGYGLFTGGLGAHAGAEALGCTVIPMSGGQTERQIQLI 188

Query: 178 QDFKPDIIMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDA 237
           QDF+PD I+ TP+Y+LT+ D M  MGIDP  TSLK  + GAEPWTQ MR  +E    I A
Sbjct: 189 QDFQPDAILATPTYLLTIADAMAHMGIDPTSTSLKYAVLGAEPWTQEMRHELEVTMNIKA 248

Query: 238 VDIYGLSEVMGPGVANECIEAKDGPVIWEDHFYPEIID---PHTGE--VLPDGSEGELVF 292
            DIYGLSEVMGPGVA E +E +DG  IWEDHF PEIID   P  G+  VL DG  GELVF
Sbjct: 249 CDIYGLSEVMGPGVAGEAVETQDGSHIWEDHFRPEIIDAFNPAVGKENVLRDGEHGELVF 308

Query: 293 TTLTKEAMPVIRYRTRDLTRLLPPTAR-SMRRMAKITGRSDDMLIIRGVNLFPTQVEELI 351
           T LTKEA+P+IRYRT+DLTRLLP TAR + RRM +ITGRSDDM+I+RGVNLFP+Q+EE+ 
Sbjct: 309 TALTKEALPIIRYRTKDLTRLLPGTARPAHRRMGRITGRSDDMIILRGVNLFPSQIEEIA 368

Query: 352 CKNPKLAPQYLLEVDK--DGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIG 409
            + P+L+P + LE+ +     MD LTVK+E      +    EQ    A+ LQ  IK  +G
Sbjct: 369 LRIPELSPHFQLELTRPEGQRMDQLTVKIERRDAVTL----EQSTTAARTLQEQIKIHVG 424

Query: 410 VSAKVHVCEPFAIERVTIGKAKRVVDRRPK 439
            S  V V EP ++ER + GK +R+ D RPK
Sbjct: 425 SSCAVDVVEPGSLER-SNGKLRRIYDLRPK 453


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: 24
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: 440
Length of database: 454
Length adjustment: 33
Effective length of query: 407
Effective length of database: 421
Effective search space:   171347
Effective search space used:   171347
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 WP_058931420.1 AU252_RS15070 (phenylacetate--CoA ligase)
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.4049526.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-200  650.2   0.0   6.4e-200  650.0   0.0    1.0  1  NCBI__GCF_001484605.1:WP_058931420.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001484605.1:WP_058931420.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  650.0   0.0  6.4e-200  6.4e-200       1     422 []      26     451 ..      26     451 .. 0.96

  Alignments for each domain:
  == domain 1  score: 650.0 bits;  conditional E-value: 6.4e-200
                             TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavp 73 
                                           e++s+del+alql+rl+ +v+ ay++vp y+++fd+ag++p dl+elsdl +fp+t+k+dlr +ypf+++avp
  NCBI__GCF_001484605.1:WP_058931420.1  26 ETISRDELEALQLTRLQHTVAYAYDRVPLYKRKFDDAGIHPTDLRELSDLGNFPFTTKEDLRAEYPFGMFAVP 98 
                                           799********************************************************************** PP

                             TIGR02155  74 rekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGa 146
                                           + +v+rvhassGttG+ptvv+yt++dl  w+++var lra+G r+g+++hnayGyGlftGGlG+h Gae lG+
  NCBI__GCF_001484605.1:WP_058931420.1  99 QSEVARVHASSGTTGRPTVVGYTKQDLADWAKLVARCLRASGVRPGMKVHNAYGYGLFTGGLGAHAGAEALGC 171
                                           ************************************************************************* PP

                             TIGR02155 147 tvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearl 219
                                           tv+p+sGGqte+q+qliqdf+pd i +tp+y+l++++++ ++gidp+++slk+a+lGaepwt++mr+ele ++
  NCBI__GCF_001484605.1:WP_058931420.1 172 TVIPMSGGQTERQIQLIQDFQPDAILATPTYLLTIADAMAHMGIDPTSTSLKYAVLGAEPWTQEMRHELEVTM 244
                                           ************************************************************************* PP

                             TIGR02155 220 gikaldiyGlseviGpGvanecvetkdGlviwedhfypeiid...petg..evlpdGeeGelvfttltkealp 287
                                           +ika diyGlsev+GpGva e+vet+dG++iwedhf peiid   p  g  +vl dGe+Gelvft+ltkealp
  NCBI__GCF_001484605.1:WP_058931420.1 245 NIKACDIYGLSEVMGPGVAGEAVETQDGSHIWEDHFRPEIIDafnPAVGkeNVLRDGEHGELVFTALTKEALP 317
                                           *****************************************844455443269******************** PP

                             TIGR02155 288 viryrtrdltrllpgtart.mrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltr.eG.al 357
                                           +iryrt+dltrllpgtar+  rrm +i+Grsdd++ilrGvn+fp+q+ee+ l++++lsph+qleltr eG ++
  NCBI__GCF_001484605.1:WP_058931420.1 318 IIRYRTKDLTRLLPGTARPaHRRMGRITGRSDDMIILRGVNLFPSQIEEIALRIPELSPHFQLELTRpEGqRM 390
                                           ******************9789********************************************954547* PP

                             TIGR02155 358 deltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                           d+lt+k+e +d +++l   eq ++ a+ ++++ik +vg s  v +vepgslers+Gk++r++d+r
  NCBI__GCF_001484605.1:WP_058931420.1 391 DQLTVKIERRD-AVTL---EQSTTAARTLQEQIKIHVGSSCAVDVVEPGSLERSNGKLRRIYDLR 451
                                           ********994.3333...46667799************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (454 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: 00:00:00.01
# Mc/sec: 18.57
//
[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