Alignments for a candidate for acs in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Halomonas desiderata SP1

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_086512010.1 BZY95_RS21920 acetate--CoA ligase

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



>NCBI__GCF_002151265.1:WP_086512010.1
          Length = 649

 Score =  954 bits (2467), Expect = 0.0
 Identities = 446/638 (69%), Positives = 527/638 (82%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           +YPVR ++AA+   D   Y+AMYQQSV +P+GFW EQAKR+DW K  T +K TSFD H+V
Sbjct: 7   VYPVRDDIAANAWIDREKYQAMYQQSVDDPEGFWAEQAKRIDWFKAPTKIKHTSFDPHNV 66

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
           DI+WF DGTLN S +CLDRHL +RGDQ AIIWEGDDP +S++++YRELH + C+ ANAL+
Sbjct: 67  DIRWFEDGTLNASVSCLDRHLEKRGDQTAIIWEGDDPKDSKHVSYRELHAKTCQLANALK 126

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
              + +GDVVT+YMPMIPEA VAMLAC RIGA+HSVVFGGFSP+ALA RI+   S++VIT
Sbjct: 127 ELGIGKGDVVTLYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDALAQRIVGADSRLVIT 186

Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245
           ADE VR GK +PLK NVD ALT   T   +KV+V KRT G+I+W + RD+WY DL+    
Sbjct: 187 ADESVRGGKHVPLKDNVDAALTRKGTEVCEKVLVVKRTGGDIEWKEGRDVWYHDLVDKQS 246

Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305
             C  +EM AE+ LFILYTSGSTG PKG++HTT GYL+YA+LTH+ +FDY+ GEVYWCTA
Sbjct: 247 ADCPAEEMNAEDPLFILYTSGSTGAPKGLKHTTGGYLVYASLTHQYIFDYQDGEVYWCTA 306

Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365
           DVGWVTGHSYIVYGPLANGATTL+FEGVP+YP   R+ +V+DKH V+ILYTAPTAIRA+M
Sbjct: 307 DVGWVTGHSYIVYGPLANGATTLMFEGVPSYPSHGRMGEVVDKHNVAILYTAPTAIRALM 366

Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425
           A G   ++ +   SLRLLGSVGEPINPEAW+WY++ +G  +CPIVDTWWQTETGG++I+P
Sbjct: 367 AHGDGVMDSSKRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGIMIAP 426

Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485
           LPGA  LKPGSAT PFFGV PAL+D+ GN ++GA +GNLVI DSWPGQAR+++GDHDRF+
Sbjct: 427 LPGAMDLKPGSATLPFFGVQPALLDSEGNELQGAVDGNLVISDSWPGQARSIWGDHDRFI 486

Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545
            TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHRMGTAEIES++VAH  VAEA
Sbjct: 487 QTYFSTYKGYYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHEAVAEA 546

Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605
           AVVG PHDIKGQGIY+YVTL  G E ++ L+ EL  WVRK+IGPIASPDVIQWAPGLPKT
Sbjct: 547 AVVGFPHDIKGQGIYIYVTLGDGVEPTDELKKELTQWVRKDIGPIASPDVIQWAPGLPKT 606

Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           RSGKIMRRILRKIA  E DGLGD STLADP VV  LIE
Sbjct: 607 RSGKIMRRILRKIAANETDGLGDTSTLADPSVVDDLIE 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: 1464
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_086512010.1 BZY95_RS21920 (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.3736.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 1022.5   0.0          0 1022.3   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086512010.1  BZY95_RS21920 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086512010.1  BZY95_RS21920 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1022.3   0.0         0         0       3     628 ..      21     644 ..      19     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1022.3 bits;  conditional E-value: 0
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhve 68 
                                               + e+y+++y+++++dpe fwa++ak+ ++w+k  +k++++s++p   +++Wfedg+ln+s+ c+drh+e
  lcl|NCBI__GCF_002151265.1:WP_086512010.1  21 DREKYQAMYQQSVDDPEGFWAEQAKR-IDWFKAPTKIKHTSFDPhnvDIRWFEDGTLNASVSCLDRHLE 88 
                                               5689*********************5.***************9988899******************** PP

                                 TIGR02188  69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRi 137
                                               kr d++aiiwegd+++ ds++++Y+el++++c+lan+lkelG+ kgd v++Y+pmipea++amlacaRi
  lcl|NCBI__GCF_002151265.1:WP_086512010.1  89 KRGDQTAIIWEGDDPK-DSKHVSYRELHAKTCQLANALKELGIGKGDVVTLYMPMIPEAAVAMLACARI 156
                                               ***************9.5*************************************************** PP

                                 TIGR02188 138 GavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtg 205
                                               Gavhsvvf+Gfs++ala+Riv a+++lvitade++Rggk+++lk++vd+al+++ +   ekvlvvkrtg
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 157 GAVHSVVFGGFSPDALAQRIVGADSRLVITADESVRGGKHVPLKDNVDAALTRKGTeVCEKVLVVKRTG 225
                                               ****************************************************99995679********* PP

                                 TIGR02188 206 eevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvky 274
                                                +++ wkegrDvw+++lv+k +sa+c++e++++edplfiLYtsGstG PkG+ httgGyl++a+lt++y
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 226 GDIE-WKEGRDVWYHDLVDK-QSADCPAEEMNAEDPLFILYTSGSTGAPKGLKHTTGGYLVYASLTHQY 292
                                               **66.**************7.************************************************ PP

                                 TIGR02188 275 vfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPta 343
                                               +fd++d++++wCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+++r+ ev++k++v+i+YtaPta
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 293 IFDYQDGEVYWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPSYPSHGRMGEVVDKHNVAILYTAPTA 361
                                               ********************************************************************* PP

                                 TIGR02188 344 iRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgv 412
                                               iRalm+ g+ ++++ +++slr+lgsvGepinpeaweWy++v+G++kcpivdtwWqtetGgi+i+plpg 
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 362 IRALMAHGDGVMDSSKRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGIMIAPLPG- 429
                                               ********************************************************************. PP

                                 TIGR02188 413 atelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkgly 481
                                               a++lkpgsatlP+fG++++++d+eg+e++   + g Lvi+++wP+++r+i+gd++rf++tYf+++kg+y
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 430 AMDLKPGSATLPFFGVQPALLDSEGNELQGAVD-GNLVISDSWPGQARSIWGDHDRFIQTYFSTYKGYY 497
                                               6****************************8888.89********************************* PP

                                 TIGR02188 482 ftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvl 550
                                               ftGDg+rrd+dGy+wi+GRvDdv+nvsGhr+gtaeies+lv+heavaeaavvg+p++ikg+ i+++v+l
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 498 FTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHEAVAEAAVVGFPHDIKGQGIYIYVTL 566
                                               ********************************************************************* PP

                                 TIGR02188 551 kegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstle 618
                                                +gve+++e l+kel+++vrk igpia+pd i++++ lPktRsGkimRR+lrkia++e + lgd+stl+
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 567 GDGVEPTDE-LKKELTQWVRKDIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAANEtDGLGDTSTLA 634
                                               ********5.************************************************999******** PP

                                 TIGR02188 619 dpsvveelke 628
                                               dpsvv++l+e
  lcl|NCBI__GCF_002151265.1:WP_086512010.1 635 DPSVVDDLIE 644
                                               ******9987 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.20
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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