Alignments for a candidate for paaK in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Cupriavidus basilensis 4G11

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate RR42_RS23755 RR42_RS23755 phenylacetate--CoA ligase

Query= BRENDA::B4EL89
         (440 letters)



>FitnessBrowser__Cup4G11:RR42_RS23755
          Length = 441

 Score =  726 bits (1873), Expect = 0.0
 Identities = 352/437 (80%), Positives = 392/437 (89%)

Query: 1   MTHPTHPAAALEPIETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKS 60
           M  P      LE IE ASRDELQALQL RLKWSLRHAYDNV HYRR FDAAGVHPDDL+ 
Sbjct: 1   MVQPIPQPGELEAIELASRDELQALQLARLKWSLRHAYDNVAHYRRAFDAAGVHPDDLRQ 60

Query: 61  LADLAKFPFSTKNDLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANV 120
           L+DLAKFP +TK DLRDNYPFGLFAVP+++VVRVHASSGTTGKPTVVGYTA+DIDTWANV
Sbjct: 61  LSDLAKFPTTTKKDLRDNYPFGLFAVPKDEVVRVHASSGTTGKPTVVGYTAKDIDTWANV 120

Query: 121 TARSIRAAGGRPGDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDF 180
           TARSIRAAGGR GDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDF
Sbjct: 121 TARSIRAAGGRRGDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDF 180

Query: 181 EPKIILVTPSYMLNLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDI 240
           EP IILVTPSYMLNLIDEM RQGM+PAESSLKIGIFGAEPWTQ +R+E+ETR GI A+DI
Sbjct: 181 EPSIILVTPSYMLNLIDEMARQGMNPAESSLKIGIFGAEPWTQGMRSEIETRAGIQAIDI 240

Query: 241 YGLSEVMGPGVACECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAM 300
           YGLSE+MGPGVA EC+E+KDGPV+WEDHFYPEIIDPVTGEVLPDGSQGELVFTSL+KEAM
Sbjct: 241 YGLSEIMGPGVASECIESKDGPVVWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLSKEAM 300

Query: 301 PVIRYRTRDLTALLPPTARAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQ 360
           P+IRYRTRDLTALL PT+R+MRRLAKITGRSDDMLI+RGVNVFPSQ+EE+++ +  LSG 
Sbjct: 301 PMIRYRTRDLTALLAPTSRSMRRLAKITGRSDDMLIIRGVNVFPSQVEELILGIARLSGN 360

Query: 361 FQITLSRDGHMDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAG 420
           +Q+ ++RDGHMD L ++VE R+E   S+ + ERA LARELQHR+KTM+GVS+ V VL AG
Sbjct: 361 YQLCITRDGHMDSLSVSVEARAEICGSLAESERAQLARELQHRVKTMIGVSTAVRVLNAG 420

Query: 421 GIPATATGKARRVIDRR 437
            I  TATGKA+RV+D R
Sbjct: 421 EIKTTATGKAQRVLDLR 437


Lambda     K      H
   0.319    0.136    0.400 

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: 732
Number of extensions: 14
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: 440
Length of database: 441
Length adjustment: 32
Effective length of query: 408
Effective length of database: 409
Effective search space:   166872
Effective search space used:   166872
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: 51 (24.3 bits)

Align candidate RR42_RS23755 RR42_RS23755 (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.18066.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-223  727.7   0.0   1.9e-223  727.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS23755  RR42_RS23755 phenylacetate--CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS23755  RR42_RS23755 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  727.5   0.0  1.9e-223  1.9e-223       1     422 []      15     437 ..      15     437 .. 0.99

  Alignments for each domain:
  == domain 1  score: 727.5 bits;  conditional E-value: 1.9e-223
                                 TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 
                                               e +s+del+alql+rlk+s+++ay+nv++yr+afdaagv+pddl++lsdlakfp t+k+dlrdnypf+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755  15 ELASRDELQALQLARLKWSLRHAYDNVAHYRRAFDAAGVHPDDLRQLSDLAKFPTTTKKDLRDNYPFGL 83 
                                               6799***************************************************************** PP

                                 TIGR02155  70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138
                                               +avp+++vvrvhassGttGkptvv+yt+kd+dtw++v ars+raaGGr+gd+lhna+GyGlftGGlG+h
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755  84 FAVPKDEVVRVHASSGTTGKPTVVGYTAKDIDTWANVTARSIRAAGGRRGDTLHNAFGYGLFTGGLGIH 152
                                               ********************************************************************* PP

                                 TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207
                                               yGae+lG++vvp+sGGqtekqvqli+df+p+ii vtpsy+l+l++e+ r+g++p++ slk++i+Gaepw
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755 153 YGAERLGCMVVPMSGGQTEKQVQLIRDFEPSIILVTPSYMLNLIDEMARQGMNPAESSLKIGIFGAEPW 221
                                               ********************************************************************* PP

                                 TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276
                                               t+ mr+e+e+r+gi+a+diyGlse++GpGva ec+e+kdG+v+wedhfypeiidp tgevlpdG++Gel
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755 222 TQGMRSEIETRAGIQAIDIYGLSEIMGPGVASECIESKDGPVVWEDHFYPEIIDPVTGEVLPDGSQGEL 290
                                               ********************************************************************* PP

                                 TIGR02155 277 vfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsp 345
                                               vft+l+kea+p+iryrtrdlt ll +t+r+mrr++ki+Grsdd+li+rGvnvfp+q+ee++l++ +ls+
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755 291 VFTSLSKEAMPMIRYRTRDLTALLAPTSRSMRRLAKITGRSDDMLIIRGVNVFPSQVEELILGIARLSG 359
                                               ********************************************************************* PP

                                 TIGR02155 346 hyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgsler.seG 413
                                               +yql +tr+G++d+l++ ve++ e   + +++++++la+++++++k+++gvs+ v++ ++g ++   +G
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755 360 NYQLCITRDGHMDSLSVSVEARAEICGSLAESERAQLARELQHRVKTMIGVSTAVRVLNAGEIKTtATG 428
                                               ****************************************************************9899* PP

                                 TIGR02155 414 kakrvvdkr 422
                                               ka+rv+d+r
  lcl|FitnessBrowser__Cup4G11:RR42_RS23755 429 KAQRVLDLR 437
                                               *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (441 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.52
//
[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:

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

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 catabolism of small carbon sources