GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Phyllobacterium brassicacearum STM 196

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_106714004.1 CU102_RS26175 acetate--CoA ligase

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



>NCBI__GCF_003010955.1:WP_106714004.1
          Length = 649

 Score =  897 bits (2317), Expect = 0.0
 Identities = 428/649 (65%), Positives = 508/649 (78%), Gaps = 3/649 (0%)

Query: 4   ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63
           + +YPV        L D  TY   Y+QS+ +P+ FW +  KR+DW KP+T VK TSF+  
Sbjct: 2   SEVYPVLASAKKDALIDNETYLNWYKQSIKDPEKFWAKHGKRIDWFKPYTKVKNTSFEGK 61

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
            V IKWF DG  NVSYNC+DRHL +RGDQ+AIIWEGD+P   + ITY EL+E+VC+ AN 
Sbjct: 62  -VAIKWFEDGVTNVSYNCIDRHLKKRGDQVAIIWEGDNPYLDKKITYNELYEQVCRLANV 120

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+   V +GD VTIYMPMIPEA  AMLACTRIGAIHSVVFGGFSP+ALAGRI+DC+S  V
Sbjct: 121 LKKHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFGGFSPDALAGRIVDCESTFV 180

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSI--QKVIVCKRTAGNIKWNQHRDIWYEDLM 241
           IT+DEG+R GK IPLK N D A+       +  + V+V +RT G   W   RD+WY + +
Sbjct: 181 ITSDEGMRGGKPIPLKDNTDKAIDIAARHHVMVKNVLVVRRTGGKTGWAPGRDLWYHEEI 240

Query: 242 KVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVY 301
                 C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY  G++Y
Sbjct: 241 ASVKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIY 300

Query: 302 WCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAI 361
           WCTADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP ++R   VIDKHKV+I YTAPTAI
Sbjct: 301 WCTADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAI 360

Query: 362 RAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGV 421
           RA+M++G   V+     SLR+LGSVGEPINPEAW+WYY+ VG +R P+VDTWWQTETGG+
Sbjct: 361 RALMSAGDEPVKKTSRKSLRILGSVGEPINPEAWEWYYQVVGDKRSPVVDTWWQTETGGI 420

Query: 422 LISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDH 481
           LI+PLPGATALKPGSATRPFFGV P LVDN G+++EG A+GNL I+DSWPGQ RT+YGDH
Sbjct: 421 LITPLPGATALKPGSATRPFFGVQPQLVDNEGDVLEGGADGNLCIIDSWPGQMRTVYGDH 480

Query: 482 DRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPK 541
            RF++TYF T+ G YFTGDG RRD+DGYYWITGRVDDVLNVSGHRMGTAE+ESA+V+H  
Sbjct: 481 KRFIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVSGHRMGTAEVESALVSHDT 540

Query: 542 VAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPG 601
           V+EAAVVG PHD+KGQGIY YVTL AG E ++ LR EL   VRKEIGPIASPD IQ+AP 
Sbjct: 541 VSEAAVVGYPHDLKGQGIYCYVTLMAGLEGTDELRKELVTHVRKEIGPIASPDKIQFAPS 600

Query: 602 LPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNV 650
           LPKTRSGKIMRRILRKIA  ++  LGD STLADP VV  +I   +   +
Sbjct: 601 LPKTRSGKIMRRILRKIAEDDFGALGDTSTLADPTVVEDMIANRQNRRI 649


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: 1459
Number of extensions: 70
Number of successful extensions: 3
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_106714004.1 CU102_RS26175 (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.1896922.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 1050.9   0.2          0 1050.7   0.2    1.0  1  NCBI__GCF_003010955.1:WP_106714004.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106714004.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1050.7   0.2         0         0       3     627 ..      18     641 ..      16     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1050.7 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++e+y ++y+++i+dpekfwak++k +++w+kp++kv+++s+e    +kWfedg +nvsync+drh++kr d+
  NCBI__GCF_003010955.1:WP_106714004.1  18 DNETYLNWYKQSIKDPEKFWAKHGK-RIDWFKPYTKVKNTSFEGkvAIKWFEDGVTNVSYNCIDRHLKKRGDQ 89 
                                           6789*********************.5**************9987789************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vaiiwegd++    +k+tY+el+++vcrlanvlk++Gvkkgdrv+iY+pmipea +amlac+RiGa+hsvvf+
  NCBI__GCF_003010955.1:WP_106714004.1  90 VAIIWEGDNPYL-DKKITYNELYEQVCRLANVLKKHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFG 161
                                           ********9996.9*********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216
                                           Gfs++ala Rivd+e+ +vit+deg+Rggk i+lk+++d+a++ a +   +v++vlvv+rtg + + w  grD
  NCBI__GCF_003010955.1:WP_106714004.1 162 GFSPDALAGRIVDCESTFVITSDEGMRGGKPIPLKDNTDKAIDIAARhhvMVKNVLVVRRTGGK-TGWAPGRD 233
                                           *****************************************9877655579*************.56****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +w++e++++ ++ ec+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaD
  NCBI__GCF_003010955.1:WP_106714004.1 234 LWYHEEIAS-VKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIYWCTAD 305
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGWvtGhsYivygPLanGattl+fegvp+yp+ srfw+vi+k+kv+ifYtaPtaiRalm +g+e vkk++++s
  NCBI__GCF_003010955.1:WP_106714004.1 306 VGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAIRALMSAGDEPVKKTSRKS 378
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lgsvGepinpeaweWyy+vvG++++p+vdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd+
  NCBI__GCF_003010955.1:WP_106714004.1 379 LRILGSVGEPINPEAWEWYYQVVGDKRSPVVDTWWQTETGGILITPLPG-ATALKPGSATRPFFGVQPQLVDN 450
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           eg+ +e +++ g L+i ++wP+++rt+ygd++rf+etYf+++kg yftGDg+rrdkdGy+wi+GRvDdv+nvs
  NCBI__GCF_003010955.1:WP_106714004.1 451 EGDVLEGGAD-GNLCIIDSWPGQMRTVYGDHKRFIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVS 522
                                           ******9988.89************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghr+gtae+esalvsh++v+eaavvg+p+++kg+ i+++v+l++g e ++e l+kel ++vrkeigpia+pdk
  NCBI__GCF_003010955.1:WP_106714004.1 523 GHRMGTAEVESALVSHDTVSEAAVVGYPHDLKGQGIYCYVTLMAGLEGTDE-LRKELVTHVRKEIGPIASPDK 594
                                           ***********************************************9995.********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           i+++++lPktRsGkimRR+lrkiae++  +lgd+stl+dp+vve+++
  NCBI__GCF_003010955.1:WP_106714004.1 595 IQFAPSLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPTVVEDMI 641
                                           ********************************************987 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 33.77
//
[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