GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Arenimonas metalli CF5-1

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_034212718.1 N787_RS08655 acetate--CoA ligase

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



>NCBI__GCF_000747155.1:WP_034212718.1
          Length = 653

 Score =  884 bits (2284), Expect = 0.0
 Identities = 429/643 (66%), Positives = 500/643 (77%), Gaps = 6/643 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           ++PV     A+     A Y  +Y  S+ +P+ FW +  +RL W KP+T  K TSF     
Sbjct: 5   IHPVPAGFEAAAALKRADYDRLYADSLRDPEAFWSQVGRRLQWSKPYTRAKDTSFALEDF 64

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDP-SESRNITYRELHEEVCKFANAL 124
            I+W+ADG LNVS NCLDRHLAERGD+ AIIWE DDP + SR I+YRELH +VC+ ANAL
Sbjct: 65  HIRWYADGQLNVSVNCLDRHLAERGDKTAIIWEADDPKTPSRRISYRELHADVCRLANAL 124

Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184
               V +GD VT+Y+PMIPEA VAMLAC RIGAIHSVVFGGFSP+++A RI DC SK+VI
Sbjct: 125 TALGVVKGDRVTLYLPMIPEAAVAMLACARIGAIHSVVFGGFSPDSIANRIADCASKLVI 184

Query: 185 TADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
           TADEG+R GK IPLKANVD+AL  P T++++ V+V + T G +     RD WY+ ++   
Sbjct: 185 TADEGLRGGKAIPLKANVDEALRKPGTNTVETVLVVRHTGGGVPMQMPRDRWYDAVVSSQ 244

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
                   M AE+ LFILYTSGSTGKPKGV HTT GYL +A+ THE VFD K  +V+WCT
Sbjct: 245 PATHDAPAMDAEDPLFILYTSGSTGKPKGVLHTTGGYLTWASYTHECVFDLKDDDVFWCT 304

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           ADVGWVTGHSY+VYGPLANGATT++FEGVP+YPD  R  + +DKH+V+I YTAPTAIRA+
Sbjct: 305 ADVGWVTGHSYVVYGPLANGATTVMFEGVPSYPDTGRFWEAVDKHQVTIFYTAPTAIRAL 364

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           M  G A V+ +   S+RLLG+VGEPINPEAW+WY++ VG ERCPIVDTWWQTETGG+LIS
Sbjct: 365 MREGDAPVKRSSRKSIRLLGTVGEPINPEAWEWYHRVVGDERCPIVDTWWQTETGGILIS 424

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           PLPGA A KPGSAT PFFGV PALVD  G  +EGA EGNLV+LDSWPGQ RT+YGDH RF
Sbjct: 425 PLPGAVATKPGSATLPFFGVQPALVDAEGKRLEGATEGNLVLLDSWPGQMRTVYGDHQRF 484

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
           +DTYFKT+ G YFTGDG RRD DGYYWITGRVDDV+NVSGHRMGTAE+ESA+V HP VAE
Sbjct: 485 IDTYFKTYPGTYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVGHPAVAE 544

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           AAVVG PHDIKGQGIY YVTL AG E +EALR EL   VRK+IGPIA+PD +QWAPGLPK
Sbjct: 545 AAVVGAPHDIKGQGIYAYVTLKAGIEPTEALRKELVAHVRKDIGPIAAPDWLQWAPGLPK 604

Query: 605 TRSGKIMRRILRKIATAEYD-----GLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA A  D     GLGD STLADPGVV  L+
Sbjct: 605 TRSGKIMRRILRKIAEAGPDGVDRAGLGDTSTLADPGVVDSLV 647


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: 1476
Number of extensions: 66
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: 653
Length adjustment: 38
Effective length of query: 613
Effective length of database: 615
Effective search space:   376995
Effective search space used:   376995
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_034212718.1 N787_RS08655 (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.644365.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-307 1006.8   0.0     2e-307 1006.5   0.0    1.0  1  NCBI__GCF_000747155.1:WP_034212718.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000747155.1:WP_034212718.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1006.5   0.0    2e-307    2e-307       4     628 ..      20     648 ..      17     649 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1006.5 bits;  conditional E-value: 2e-307
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                             +y +ly+++ +dpe+fw++ ++ +l+w kp+++ +d+s++    +++W++dg+lnvs+nc+drh+++r dk
  NCBI__GCF_000747155.1:WP_034212718.1  20 RADYDRLYADSLRDPEAFWSQVGR-RLQWSKPYTRAKDTSFALedfHIRWYADGQLNVSVNCLDRHLAERGDK 91 
                                           578********************9.5**************9877789************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwe+d++++ sr+++Y+el+++vcrlan+l++lGv kgdrv++Ylpmipea++amlacaRiGa+hsvvf+
  NCBI__GCF_000747155.1:WP_034212718.1  92 TAIIWEADDPKTPSRRISYRELHADVCRLANALTALGVVKGDRVTLYLPMIPEAAVAMLACARIGAIHSVVFG 164
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs++++a+Ri d+ +klvitadeglRggk+i+lk++vdeal+k  + +ve+vlvv++tg  v  ++  rD w
  NCBI__GCF_000747155.1:WP_034212718.1 165 GFSPDSIANRIADCASKLVITADEGLRGGKAIPLKANVDEALRKPGTnTVETVLVVRHTGGGVP-MQMPRDRW 236
                                           ********************************************9988**************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           ++ +v++ ++a++++ ++d+edplfiLYtsGstGkPkGvlhttgGyl++a++t++ vfd+kd+d+fwCtaDvG
  NCBI__GCF_000747155.1:WP_034212718.1 237 YDAVVSS-QPATHDAPAMDAEDPLFILYTSGSTGKPKGVLHTTGGYLTWASYTHECVFDLKDDDVFWCTADVG 308
                                           ******6.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsY+vygPLanGatt++fegvp+ypd++rfwe ++k++vtifYtaPtaiRalm++g++ vk+ +++s+r
  NCBI__GCF_000747155.1:WP_034212718.1 309 WVTGHSYVVYGPLANGATTVMFEGVPSYPDTGRFWEAVDKHQVTIFYTAPTAIRALMREGDAPVKRSSRKSIR 381
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lg+vGepinpeaweWy++vvG+e+cpivdtwWqtetGgili+plpg a+++kpgsatlP+fG+++++vd eg
  NCBI__GCF_000747155.1:WP_034212718.1 382 LLGTVGEPINPEAWEWYHRVVGDERCPIVDTWWQTETGGILISPLPG-AVATKPGSATLPFFGVQPALVDAEG 453
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           k++e  +e g Lv+ ++wP+++rt+ygd++rf++tYfk+++g+yftGDg+rrd+dGy+wi+GRvDdvinvsGh
  NCBI__GCF_000747155.1:WP_034212718.1 454 KRLEGATE-GNLVLLDSWPGQMRTVYGDHQRFIDTYFKTYPGTYFTGDGCRRDADGYYWITGRVDDVINVSGH 525
                                           ****8777.79************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtae+esalv h+avaeaavvg+p++ikg+ i+a+v+lk+g+e++e +l+kel ++vrk igpia+pd ++
  NCBI__GCF_000747155.1:WP_034212718.1 526 RMGTAEVESALVGHPAVAEAAVVGAPHDIKGQGIYAYVTLKAGIEPTE-ALRKELVAHVRKDIGPIAAPDWLQ 597
                                           ***********************************************9.5*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaeg......eellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkiae       +  lgd+stl+dp vv++l +
  NCBI__GCF_000747155.1:WP_034212718.1 598 WAPGLPKTRSGKIMRRILRKIAEAgpdgvdRAGLGDTSTLADPGVVDSLVN 648
                                           **********************9622222135689************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (653 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: 00:00:00.01
# Mc/sec: 22.83
//
[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