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_106712619.1 CU102_RS18670 acetate--CoA ligase

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



>NCBI__GCF_003010955.1:WP_106712619.1
          Length = 650

 Score =  897 bits (2319), Expect = 0.0
 Identities = 430/639 (67%), Positives = 506/639 (79%), Gaps = 3/639 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           +YPV        L D  TY   Y+QS+ +P+ FW +  KR+DW KP+T VK TSF+   V
Sbjct: 5   VYPVLASAKKDALIDNETYLNWYKQSIKDPEKFWAKHGKRIDWFKPYTKVKNTSFEGK-V 63

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
            IKWF DG  NVSYNC+DRHL +RGDQ+AIIWEGD+P   + ITY EL+E+VC+ AN L+
Sbjct: 64  AIKWFEDGVTNVSYNCIDRHLKKRGDQVAIIWEGDNPYLDKKITYNELYEQVCRLANVLK 123

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
              V +GD VTIYMPMIPEA  AMLACTRIGAIHSVVFGGFSP+ALAGRI+DC+S  VIT
Sbjct: 124 KHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFGGFSPDALAGRIVDCESTFVIT 183

Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSI--QKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           +DEG+R GK IPLK N D A+       +  + V+V +RT G   W   RD+WY + +  
Sbjct: 184 SDEGMRGGKPIPLKDNTDKAIDIAARHHVMVKNVLVVRRTGGKTGWAPGRDLWYHEEIAS 243

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY  G++YWC
Sbjct: 244 VKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIYWC 303

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP ++R   VIDKHKV+I YTAPTAIRA
Sbjct: 304 TADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAIRA 363

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M++G   V+     SLR+LGSVGEPINPEAW+WYY+ VG +R PIVDTWWQTETGG+LI
Sbjct: 364 LMSAGDEPVKKTSRKSLRILGSVGEPINPEAWEWYYQVVGDKRSPIVDTWWQTETGGILI 423

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           +PLPGATALKPGSATRPFFGV P LVDN G+++EGAA+GNL I+DSWPGQ RT+YGDH R
Sbjct: 424 TPLPGATALKPGSATRPFFGVQPQLVDNEGDVLEGAADGNLCIIDSWPGQMRTVYGDHKR 483

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
           F++TYF T+ G YFTGDG RRD+DGYYWITGRVDDVLNVSGHRMGTAE+ESA+V+H  V+
Sbjct: 484 FIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVSGHRMGTAEVESALVSHDTVS 543

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY YVTL AG + ++ LR EL   VRKEIGPIASPD IQ+AP LP
Sbjct: 544 EAAVVGYPHDLKGQGIYCYVTLMAGLDGTDELRKELVTHVRKEIGPIASPDKIQFAPSLP 603

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           KTRSGKIMRRILRKIA  ++  LGD STLADP VV  LI
Sbjct: 604 KTRSGKIMRRILRKIAEDDFGALGDTSTLADPAVVDDLI 642


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: 1473
Number of extensions: 71
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: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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_106712619.1 CU102_RS18670 (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.2263171.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 1050.3   0.1          0 1050.1   0.1    1.0  1  NCBI__GCF_003010955.1:WP_106712619.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712619.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1050.1   0.1         0         0       3     628 ..      19     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1050.1 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_106712619.1  19 DNETYLNWYKQSIKDPEKFWAKHGK-RIDWFKPYTKVKNTSFEGkvAIKWFEDGVTNVSYNCIDRHLKKRGDQ 90 
                                           6789*********************.5**************9987789************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vaiiwegd++    +k+tY+el+++vcrlanvlk++Gvkkgdrv+iY+pmipea +amlac+RiGa+hsvvf+
  NCBI__GCF_003010955.1:WP_106712619.1  91 VAIIWEGDNPYL-DKKITYNELYEQVCRLANVLKKHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFG 162
                                           ********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_106712619.1 163 GFSPDALAGRIVDCESTFVITSDEGMRGGKPIPLKDNTDKAIDIAARhhvMVKNVLVVRRTGGK-TGWAPGRD 234
                                           *****************************************9877655579*************.56****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +w++e++++ ++ ec+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaD
  NCBI__GCF_003010955.1:WP_106712619.1 235 LWYHEEIAS-VKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIYWCTAD 306
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGWvtGhsYivygPLanGattl+fegvp+yp+ srfw+vi+k+kv+ifYtaPtaiRalm +g+e vkk++++s
  NCBI__GCF_003010955.1:WP_106712619.1 307 VGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAIRALMSAGDEPVKKTSRKS 379
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lgsvGepinpeaweWyy+vvG++++pivdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd+
  NCBI__GCF_003010955.1:WP_106712619.1 380 LRILGSVGEPINPEAWEWYYQVVGDKRSPIVDTWWQTETGGILITPLPG-ATALKPGSATRPFFGVQPQLVDN 451
                                           *************************************************.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_106712619.1 452 EGDVLEGAAD-GNLCIIDSWPGQMRTVYGDHKRFIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVS 523
                                           *****98777.79************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghr+gtae+esalvsh++v+eaavvg+p+++kg+ i+++v+l++g + ++ el+kel ++vrkeigpia+pdk
  NCBI__GCF_003010955.1:WP_106712619.1 524 GHRMGTAEVESALVSHDTVSEAAVVGYPHDLKGQGIYCYVTLMAGLDGTD-ELRKELVTHVRKEIGPIASPDK 595
                                           ***********************************************999.5********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i+++++lPktRsGkimRR+lrkiae++  +lgd+stl+dp+vv++l++
  NCBI__GCF_003010955.1:WP_106712619.1 596 IQFAPSLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPAVVDDLIA 643
                                           ********************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (650 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: 19.38
//
[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