Alignments for a candidate for paaK in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Herbaspirillum seropedicae SmR1

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate HSERO_RS20655 HSERO_RS20655 phenylacetate-CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__HerbieS:HSERO_RS20655
          Length = 446

 Score =  688 bits (1776), Expect = 0.0
 Identities = 330/439 (75%), Positives = 384/439 (87%), Gaps = 4/439 (0%)

Query: 1   MPVKTPSPGDLEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKS 60
           M ++ P PG+LEPIE AS+DEL+ALQL+RLKWS+RHAY+NVPHYR AFD  GVHPDDLKS
Sbjct: 1   MTIRIPQPGELEPIETASRDELQALQLQRLKWSLRHAYDNVPHYRNAFDQAGVHPDDLKS 60

Query: 61  LADLAKFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATV 120
           L+DL++FPFT K DLRD+YPFGMFAVPRE+V RVHASSGTTGKPTVVGYT  DIDTWATV
Sbjct: 61  LSDLSRFPFTTKKDLRDHYPFGMFAVPREQVVRVHASSGTTGKPTVVGYTQNDIDTWATV 120

Query: 121 VARSIRASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDF 180
           VARSIRA+GGR GD+V I+YGYGLFTGGLGAHYGAEKLGCTV+PMSGGQTEKQ+QLI+DF
Sbjct: 121 VARSIRAAGGRRGDIVQISYGYGLFTGGLGAHYGAEKLGCTVIPMSGGQTEKQVQLIRDF 180

Query: 181 KPDIIMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDI 240
           KP IIMVTPSYML V++E +R G+DP  +SLKVGIFGAEPWT AMR  ++ RAG+DAVDI
Sbjct: 181 KPSIIMVTPSYMLNVIEEFQRQGMDPASSSLKVGIFGAEPWTDAMRREIQQRAGLDAVDI 240

Query: 241 YGLSEVMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAM 300
           YGLSEVMGPGVA+ECIE+KDGPVIWEDHFYPEIIDP TGEVLPDG EGELVFT+L+KEA+
Sbjct: 241 YGLSEVMGPGVASECIESKDGPVIWEDHFYPEIIDPDTGEVLPDGVEGELVFTSLSKEAL 300

Query: 301 PVIRYRTRDLTRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQ 360
           P+IRYRTRDLTRLLPPT+RSMRR+ KITGRSDDMLIIRGVN+FPTQ+EELI K P+LAPQ
Sbjct: 301 PMIRYRTRDLTRLLPPTSRSMRRIGKITGRSDDMLIIRGVNVFPTQIEELILKLPQLAPQ 360

Query: 361 YLLEVDKDGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPF 420
           Y L++++ GHMD+++V  E+  + +     E  EAL KELQH IKT++G+S KV V    
Sbjct: 361 YQLQIERHGHMDSMSVFAELREDVS----NEHVEALEKELQHSIKTYVGISTKVTVVPAG 416

Query: 421 AIERVTIGKAKRVVDRRPK 439
            IER ++GKAKRV+D R K
Sbjct: 417 MIERTSVGKAKRVIDNRKK 435


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: 732
Number of extensions: 20
Number of successful extensions: 2
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: 446
Length adjustment: 32
Effective length of query: 408
Effective length of database: 414
Effective search space:   168912
Effective search space used:   168912
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 HSERO_RS20655 HSERO_RS20655 (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.19937.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.3e-227  738.6   0.0   9.5e-227  738.4   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20655  HSERO_RS20655 phenylacetate-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20655  HSERO_RS20655 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  738.4   0.0  9.5e-227  9.5e-227       1     422 []      15     433 ..      15     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 738.4 bits;  conditional E-value: 9.5e-227
                                  TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfd 68 
                                                e++s+del+alql+rlk+s+++ay+nvp+yr+afd+agv+pddlk+lsdl +fp+t+k+dlrd ypf+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655  15 ETASRDELQALQLQRLKWSLRHAYDNVPHYRNAFDQAGVHPDDLKSLSDLSRFPFTTKKDLRDHYPFG 82 
                                                89****************************************************************** PP

                                  TIGR02155  69 llavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlG 136
                                                ++avpre+vvrvhassGttGkptvv+ytq+d+dtw++vvars+raaGGr+gd++ ++yGyGlftGGlG
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655  83 MFAVPREQVVRVHASSGTTGKPTVVGYTQNDIDTWATVVARSIRAAGGRRGDIVQISYGYGLFTGGLG 150
                                                ******************************************************************** PP

                                  TIGR02155 137 vhyGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGa 204
                                                +hyGaeklG+tv+p+sGGqtekqvqli+dfkp+ii+vtpsy+l+++ee++r+g+dp++ slkv+i+Ga
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655 151 AHYGAEKLGCTVIPMSGGQTEKQVQLIRDFKPSIIMVTPSYMLNVIEEFQRQGMDPASSSLKVGIFGA 218
                                                ******************************************************************** PP

                                  TIGR02155 205 epwteamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGe 272
                                                epwt+amr+e+++r+g++a+diyGlsev+GpGva ec+e+kdG+viwedhfypeiidp+tgevlpdG 
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655 219 EPWTDAMRREIQQRAGLDAVDIYGLSEVMGPGVASECIESKDGPVIWEDHFYPEIIDPDTGEVLPDGV 286
                                                ******************************************************************** PP

                                  TIGR02155 273 eGelvfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkl 340
                                                eGelvft+l+kealp+iryrtrdltrllp+t+r+mrr+ ki+Grsdd+li+rGvnvfptq+ee++lkl
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655 287 EGELVFTSLSKEALPMIRYRTRDLTRLLPPTSRSMRRIGKITGRSDDMLIIRGVNVFPTQIEELILKL 354
                                                ******************************************************************** PP

                                  TIGR02155 341 dklsphyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgsl 408
                                                ++l+p+yql+++r+G++d++++ +el+++ ++    e+ ++l k+++++ik+ vg+s++v++v +g +
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655 355 PQLAPQYQLQIERHGHMDSMSVFAELREDVSN----EHVEALEKELQHSIKTYVGISTKVTVVPAGMI 418
                                                ***************************55443....456679************************** PP

                                  TIGR02155 409 er.seGkakrvvdkr 422
                                                er s Gkakrv+d+r
  lcl|FitnessBrowser__HerbieS:HSERO_RS20655 419 ERtSVGKAKRVIDNR 433
                                                **999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (446 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: 00:00:00.02
# Mc/sec: 7.13
//
[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