GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halomonas smyrnensis AAD6

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_016853633.1 UYS_RS0201040 acetate--CoA ligase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>NCBI__GCF_000265245.1:WP_016853633.1
          Length = 649

 Score =  941 bits (2432), Expect = 0.0
 Identities = 442/638 (69%), Positives = 523/638 (81%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           +YPV  + AA    D+ATY+AMYQ+S+ +P+GFW EQA+ LDW K  + +K T FD   V
Sbjct: 7   VYPVPDDFAAKAWADKATYQAMYQRSLDDPEGFWAEQAECLDWFKAPSKIKHTVFDPQDV 66

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
           DI+WF DG LNVS NCLDRHL  RGDQ AIIWEGDDP +S+ +TYR+LHE  C+ ANAL+
Sbjct: 67  DIRWFEDGRLNVSSNCLDRHLETRGDQTAIIWEGDDPEDSKTLTYRQLHERTCQLANALK 126

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
           G  V RGD VT+YMPMIPEA +AMLAC RIGA+HSVVFGGFSP+ALA R+ D  S+VVIT
Sbjct: 127 GMGVKRGDTVTLYMPMIPEAAMAMLACARIGAVHSVVFGGFSPDALAQRVKDAGSRVVIT 186

Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245
           ADE VR GK++PLK NVD ALT   +   +KV+V +RT G I W++ RD+W+ + +    
Sbjct: 187 ADESVRGGKQVPLKDNVDAALTREGSDVCEKVLVVQRTGGEIDWHEGRDLWFHEQVDPQS 246

Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305
           T C  +EMGAE+ LFILYTSGSTG PKG++HTT GYLL+AALTH  VFDY  G++YWCTA
Sbjct: 247 TDCPAEEMGAEDPLFILYTSGSTGAPKGLKHTTGGYLLHAALTHRYVFDYHDGDIYWCTA 306

Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365
           DVGWVTGHSYIVYGPLANGATTL+FEGVP+YP   R+ +++DKH+V+ILYTAPTA+RA+M
Sbjct: 307 DVGWVTGHSYIVYGPLANGATTLMFEGVPSYPTNGRMGEIVDKHRVNILYTAPTAVRALM 366

Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425
           A G   ++ +   SLRLLGSVGEPINPEAW+W+++ +G ERCPIVDTWWQTETGG++I+P
Sbjct: 367 AHGDDVMDSSSRDSLRLLGSVGEPINPEAWEWFHRVIGNERCPIVDTWWQTETGGIMIAP 426

Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485
           LPGAT LKPGSAT PFFGV PALVDN GN++EGA EGNLV+LD+WPGQAR+++ +H+RF+
Sbjct: 427 LPGATDLKPGSATLPFFGVQPALVDNEGNILEGATEGNLVMLDAWPGQARSIWNNHERFL 486

Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545
            TYF T+ GMYFTGDG RRDEDGYYWITGRVDDVLNVSGHRMGTAEIES++VAH  VAEA
Sbjct: 487 QTYFSTYKGMYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHESVAEA 546

Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605
           AVVG PHDIKGQGIY+YVTL    E S+ L+  L  WVRK+IGPIASPDVIQWAPGLPKT
Sbjct: 547 AVVGFPHDIKGQGIYIYVTLADDVEPSDELKKALTQWVRKDIGPIASPDVIQWAPGLPKT 606

Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           RSGKIMRRILRKIA  E DGLGD STLADP VV  LIE
Sbjct: 607 RSGKIMRRILRKIAANECDGLGDTSTLADPSVVDDLIE 644


Lambda     K      H
   0.318    0.135    0.418 

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: 1463
Number of extensions: 52
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: 651
Length of database: 649
Length adjustment: 38
Effective length of query: 613
Effective length of database: 611
Effective search space:   374543
Effective search space used:   374543
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_016853633.1 UYS_RS0201040 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# 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/TIGR02188.hmm
# target sequence database:        /tmp/gapView.1681164.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1013.1   0.0          0 1012.9   0.0    1.0  1  NCBI__GCF_000265245.1:WP_016853633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000265245.1:WP_016853633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1012.9   0.0         0         0       4     628 ..      22     644 ..      19     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1012.9 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                             +y+++y+++ +dpe fwa++a+  l+w+k  +k++++ ++p   +++Wfedg+lnvs nc+drh+e+r d+
  NCBI__GCF_000265245.1:WP_016853633.1  22 KATYQAMYQRSLDDPEGFWAEQAE-CLDWFKAPSKIKHTVFDPqdvDIRWFEDGRLNVSSNCLDRHLETRGDQ 93 
                                           679********************9.6************999887789************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwegd+++ ds++ltY++l++++c+lan+lk +Gvk+gd+v++Y+pmipea++amlacaRiGavhsvvf+
  NCBI__GCF_000265245.1:WP_016853633.1  94 TAIIWEGDDPE-DSKTLTYRQLHERTCQLANALKGMGVKRGDTVTLYMPMIPEAAMAMLACARIGAVHSVVFG 165
                                           ********998.6************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs++ala+R++da +++vitade++Rggk+++lk++vd+al+++ +   ekvlvv+rtg e+  w+egrD+w
  NCBI__GCF_000265245.1:WP_016853633.1 166 GFSPDALAQRVKDAGSRVVITADESVRGGKQVPLKDNVDAALTREGSdVCEKVLVVQRTGGEID-WHEGRDLW 237
                                           *******************************************99996779***********66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           ++e v+  +s++c++e++++edplfiLYtsGstG PkG+ httgGyll+aalt++yvfd++d+di+wCtaDvG
  NCBI__GCF_000265245.1:WP_016853633.1 238 FHEQVD-PQSTDCPAEEMGAEDPLFILYTSGSTGAPKGLKHTTGGYLLHAALTHRYVFDYHDGDIYWCTADVG 309
                                           ******.6***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsYivygPLanGattl+fegvp+yp+++r+ e+++k++v+i+YtaPta+Ralm+ g++++++ +++slr
  NCBI__GCF_000265245.1:WP_016853633.1 310 WVTGHSYIVYGPLANGATTLMFEGVPSYPTNGRMGEIVDKHRVNILYTAPTAVRALMAHGDDVMDSSSRDSLR 382
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lgsvGepinpeaweW+++v+G+e+cpivdtwWqtetGgi+i+plpg at+lkpgsatlP+fG+++++vd+eg
  NCBI__GCF_000265245.1:WP_016853633.1 383 LLGSVGEPINPEAWEWFHRVIGNERCPIVDTWWQTETGGIMIAPLPG-ATDLKPGSATLPFFGVQPALVDNEG 454
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           + +e  +e g Lv+ ++wP+++r+i++++erf +tYf+++kg+yftGDg+rrd+dGy+wi+GRvDdv+nvsGh
  NCBI__GCF_000265245.1:WP_016853633.1 455 NILEGATE-GNLVMLDAWPGQARSIWNNHERFLQTYFSTYKGMYFTGDGCRRDEDGYYWITGRVDDVLNVSGH 526
                                           ****8777.79************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtaeies+lv+he+vaeaavvg+p++ikg+ i+++v+l + ve+++e l+k l+++vrk igpia+pd i+
  NCBI__GCF_000265245.1:WP_016853633.1 527 RMGTAEIESSLVAHESVAEAAVVGFPHDIKGQGIYIYVTLADDVEPSDE-LKKALTQWVRKDIGPIASPDVIQ 598
                                           ************************************************5.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkia++e + lgd+stl+dpsvv++l+e
  NCBI__GCF_000265245.1:WP_016853633.1 599 WAPGLPKTRSGKIMRRILRKIAANEcDGLGDTSTLADPSVVDDLIE 644
                                           ******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 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: 00:00:00.02
# Mc/sec: 18.26
//
[ok]

This GapMind analysis is from Sep 24 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