GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinicella litoralis KMM 3900

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_099018876.1 CCS90_RS07185 acetate--CoA ligase

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



>NCBI__GCF_002591915.1:WP_099018876.1
          Length = 646

 Score =  900 bits (2325), Expect = 0.0
 Identities = 435/637 (68%), Positives = 495/637 (77%), Gaps = 2/637 (0%)

Query: 7   YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YPV PE A  TL D   Y +MYQQS+ N + FW    KRLDWIKP+  +K  SFD   + 
Sbjct: 5   YPVHPEFATHTLCDNDKYLSMYQQSIENNEAFWGLHGKRLDWIKPYIQIKDVSFDQQDLH 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126
           IKWFADG LNVSYNC+DRHL  + DQ AIIWEGD+P+ES+NI+Y ELH+EV +FAN L+ 
Sbjct: 65  IKWFADGQLNVSYNCIDRHLPTKADQTAIIWEGDNPAESKNISYAELHQEVGRFANTLKK 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
             V +GD VT+YMPMIPEA  AMLAC RIGAIHSVVFGGFSPEAL  RII+CKSK+VITA
Sbjct: 125 LGVIKGDRVTLYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALGDRIINCKSKLVITA 184

Query: 187 DEGVRAGKKIPLKANVDDALTNPETSS-IQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245
           D GVR  K I LKANVD A         ++ V+V K     + W  H D WY ++ +   
Sbjct: 185 DRGVRGAKSIGLKANVDKATKKAGVKDYLESVLVIKTADHEVDWYDH-DHWYHEVSQSVD 243

Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305
           T C P  M AE+ LFILYTSGSTG+PKGV HT+ GYLLYA++THE VFD +PG+VYWCTA
Sbjct: 244 TFCEPAIMNAEDPLFILYTSGSTGQPKGVLHTSGGYLLYASMTHEYVFDIQPGDVYWCTA 303

Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365
           DVGW+TGHSY+VYGPLANG TTL+FEGVPNYPD +R  ++ DKH+V+I YTAPTAIRA+M
Sbjct: 304 DVGWITGHSYVVYGPLANGGTTLMFEGVPNYPDHSRFWQICDKHQVNICYTAPTAIRALM 363

Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425
             G   V+     SLR+LGSVGEPINPEAW WYY+ VG+ R PIVDTWWQTETGG++ISP
Sbjct: 364 KEGDEPVKSTSRKSLRVLGSVGEPINPEAWKWYYEVVGEARSPIVDTWWQTETGGIMISP 423

Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485
           LPGATALKPGSATRPFFG+ PAL+DN GN + G A GNLVI DSWPGQ RT+YGDH RF 
Sbjct: 424 LPGATALKPGSATRPFFGIKPALLDNEGNELNGVASGNLVITDSWPGQMRTVYGDHARFY 483

Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545
            TYF  F  +Y TGDGA+RDEDGYYWITGR DDVLNVSGHRMGTAE+ESA+VAHP VAEA
Sbjct: 484 TTYFAAFKNVYTTGDGAKRDEDGYYWITGRTDDVLNVSGHRMGTAEVESALVAHPAVAEA 543

Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605
           AVVG PHDIKGQGIY YVTL  G   SE L  EL NWVR EIGPIA+PD IQWAPGLPKT
Sbjct: 544 AVVGYPHDIKGQGIYAYVTLVNGMAESETLLSELVNWVRSEIGPIATPDKIQWAPGLPKT 603

Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           RSGKIMRRILRKIA  E+  LGD STLA+P VV +LI
Sbjct: 604 RSGKIMRRILRKIAANEHKNLGDTSTLAEPEVVVNLI 640


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: 1408
Number of extensions: 59
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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_099018876.1 CCS90_RS07185 (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.2840434.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.4e-306 1001.4   0.1   8.6e-306 1001.2   0.1    1.0  1  NCBI__GCF_002591915.1:WP_099018876.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002591915.1:WP_099018876.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1001.2   0.1  8.6e-306  8.6e-306       3     628 ..      18     641 ..      16     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1001.2 bits;  conditional E-value: 8.6e-306
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           ++++y ++y+++ie+ e+fw+ ++k +l+w+kp+ +++d s+++   ++kWf+dg+lnvsync+drh+ +++d
  NCBI__GCF_002591915.1:WP_099018876.1  18 DNDKYLSMYQQSIENNEAFWGLHGK-RLDWIKPYIQIKDVSFDQqdlHIKWFADGQLNVSYNCIDRHLPTKAD 89 
                                           5789********************9.5************999887789************************* PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           ++aiiwegd++ e s++++Yael++ev r+an+lk+lGv kgdrv++Y+pmipea++amlacaRiGa+hsvvf
  NCBI__GCF_002591915.1:WP_099018876.1  90 QTAIIWEGDNPAE-SKNISYAELHQEVGRFANTLKKLGVIKGDRVTLYMPMIPEAAYAMLACARIGAIHSVVF 161
                                           *********9996.*********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee..svekvlvvkrtgeevaewkegrD 216
                                           +Gfs+eal +Ri+++++klvitad g+Rg k+i lk++vd+a +ka     +e+vlv+k +++ev  w  ++D
  NCBI__GCF_002591915.1:WP_099018876.1 162 GGFSPEALGDRIINCKSKLVITADRGVRGAKSIGLKANVDKATKKAGVkdYLESVLVIKTADHEVD-WY-DHD 232
                                           ********************************************9987668*************76.87.79* PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +w++e+ ++ +++ cep+ +++edplfiLYtsGstG+PkGvlht+gGyll+a++t++yvfdi+++d++wCtaD
  NCBI__GCF_002591915.1:WP_099018876.1 233 HWYHEVSQS-VDTFCEPAIMNAEDPLFILYTSGSTGQPKGVLHTSGGYLLYASMTHEYVFDIQPGDVYWCTAD 304
                                           ********5.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGW+tGhsY+vygPLanG ttl+fegvp+ypd+srfw++++k++v+i YtaPtaiRalmk+g+e vk+++++s
  NCBI__GCF_002591915.1:WP_099018876.1 305 VGWITGHSYVVYGPLANGGTTLMFEGVPNYPDHSRFWQICDKHQVNICYTAPTAIRALMKEGDEPVKSTSRKS 377
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lrvlgsvGepinpeaw+WyyevvG+ ++pivdtwWqtetGgi+i+plpg at+lkpgsat+P+fGi+++++d+
  NCBI__GCF_002591915.1:WP_099018876.1 378 LRVLGSVGEPINPEAWKWYYEVVGEARSPIVDTWWQTETGGIMISPLPG-ATALKPGSATRPFFGIKPALLDN 449
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           eg+e++  ++ g Lvi+++wP+++rt+ygd+ rf +tYf ++k++y tGDga+rd+dGy+wi+GR+Ddv+nvs
  NCBI__GCF_002591915.1:WP_099018876.1 450 EGNELNGVAS-GNLVITDSWPGQMRTVYGDHARFYTTYFAAFKNVYTTGDGAKRDEDGYYWITGRTDDVLNVS 521
                                           *****98777.89************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghr+gtae+esalv+h+avaeaavvg+p++ikg+ i+a+v+l +g++e+e +l +el ++vr+eigpia+pdk
  NCBI__GCF_002591915.1:WP_099018876.1 522 GHRMGTAEVESALVAHPAVAEAAVVGYPHDIKGQGIYAYVTLVNGMAESE-TLLSELVNWVRSEIGPIATPDK 593
                                           ***********************************************999.5********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i++++ lPktRsGkimRR+lrkia++e ++lgd+stl++p+vv +l++
  NCBI__GCF_002591915.1:WP_099018876.1 594 IQWAPGLPKTRSGKIMRRILRKIAANEhKNLGDTSTLAEPEVVVNLIN 641
                                           ***************************99*************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 28.65
//
[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