GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Dyella japonica UNC79MFTsu3.2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate N515DRAFT_3075 N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__Dyella79:N515DRAFT_3075
          Length = 646

 Score =  909 bits (2350), Expect = 0.0
 Identities = 432/640 (67%), Positives = 514/640 (80%)

Query: 4   ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63
           + +YPV+PE AA     +  Y+ +Y++SV +P+GFW    +RL+W +  + +K  S+D  
Sbjct: 2   SKVYPVKPEFAAKARISKEDYERLYEESVRDPEGFWGRIGERLEWHRKPSKIKNVSYDPK 61

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
           ++ I+W+ DG LNVS NCLDRHLA RGD+ AII+EGDDP+ESR++TYRELH EVCKFAN 
Sbjct: 62  NLHIRWYEDGELNVSANCLDRHLASRGDKTAIIFEGDDPNESRHLTYRELHAEVCKFANT 121

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+   V +GD V IYMPMIPEA VAMLAC RIGA+HSVVFGGFSP++LAGRI D  +KVV
Sbjct: 122 LKNLGVAKGDRVAIYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDSLAGRIADSTAKVV 181

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           +TADEGVR GKKIPLKANVD AL  P T+S++ VIV +RT   +     RD +Y  LM+ 
Sbjct: 182 VTADEGVRGGKKIPLKANVDAALERPGTNSVETVIVVRRTGSAVPMQSPRDRYYHVLMEG 241

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P  + AE  LFILYTSGSTGKPKGV HT+ GYL++A  THE VFD +  +VYWC
Sbjct: 242 QSADCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSGGYLVFAGFTHEMVFDLREDDVYWC 301

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSY+VYGPLANGATT++F+GVPNYPD +R   V+DKHKV++ YTAPTAIRA
Sbjct: 302 TADVGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNVVDKHKVTLFYTAPTAIRA 361

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G A V+ A  +SLRLLGSVGEPINPEAW+WYY+ VG ERCPIVDTWWQTETGG++I
Sbjct: 362 LMREGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVDTWWQTETGGIMI 421

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           +PL GA   KPGSAT+PFFG+ PA+VD  G ++EGA EGNLVI DSWPGQ RT+YGDH R
Sbjct: 422 TPLAGAIDAKPGSATKPFFGIRPAVVDAGGAVLEGATEGNLVIADSWPGQMRTVYGDHQR 481

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
           FV+TYF  + G YFTGDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+HPKVA
Sbjct: 482 FVETYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVA 541

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PH+IKGQGIY YVTL AGE+ S+ LR EL  WVRKEIGPIA+PD +QWAPGLP
Sbjct: 542 EAAVVGCPHEIKGQGIYAYVTLIAGEQGSDELRKELVAWVRKEIGPIATPDYLQWAPGLP 601

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKI   + D LGDISTLADP VV +L+E
Sbjct: 602 KTRSGKIMRRILRKIGENQPDQLGDISTLADPSVVKNLVE 641


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: 1422
Number of extensions: 75
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 N515DRAFT_3075 N515DRAFT_3075 (acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.6130.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 1024.9   0.0          0 1024.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  N515DRAFT_3075 acetyl-coenzyme A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1024.7   0.0         0         0       3     628 ..      18     641 ..      16     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1024.7 bits;  conditional E-value: 0
                                    TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdr 65 
                                                  + e+y++lyee+++dpe fw++ ++ +lew+++ +k+++ s +p   +++W+edgelnvs+nc+dr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  18 SKEDYERLYEESVRDPEGFWGRIGE-RLEWHRKPSKIKNVSYDPknlHIRWYEDGELNVSANCLDR 82 
                                                  5789********************9.5************9998877899***************** PP

                                    TIGR02188  66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviam 131
                                                  h+++r dk+aii+egd+++e sr+ltY+el++evc++an+lk+lGv kgdrvaiY+pmipea++am
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  83 HLASRGDKTAIIFEGDDPNE-SRHLTYRELHAEVCKFANTLKNLGVAKGDRVAIYMPMIPEAAVAM 147
                                                  ******************96.********************************************* PP

                                    TIGR02188 132 lacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.sve 196
                                                  lacaRiGavhsvvf+Gfs+++la Ri d++ak+v+tadeg+Rggk+i+lk++vd+ale+  + sve
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 148 LACARIGAVHSVVFGGFSPDSLAGRIADSTAKVVVTADEGVRGGKKIPLKANVDAALERPGTnSVE 213
                                                  ***********************************************************9988*** PP

                                    TIGR02188 197 kvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttg 262
                                                  +v+vv+rtg+ v  +++ rD +++ l+e ++sa+c+p+++++e+plfiLYtsGstGkPkGvlht+g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 214 TVIVVRRTGSAVP-MQSPRDRYYHVLME-GQSADCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSG 277
                                                  ***********66.**************.6************************************ PP

                                    TIGR02188 263 GylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwev 328
                                                  Gyl+ a  t+++vfd++++d++wCtaDvGWvtGhsY+vygPLanGatt++f+gvp+ypd+srfw+v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 278 GYLVFAGFTHEMVFDLREDDVYWCTADVGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNV 343
                                                  ****************************************************************** PP

                                    TIGR02188 329 iekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivd 394
                                                  ++k+kvt fYtaPtaiRalm++ge+ vkk ++ slr+lgsvGepinpeaweWyy+vvG+e+cpivd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 344 VDKHKVTLFYTAPTAIRALMREGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVD 409
                                                  ****************************************************************** PP

                                    TIGR02188 395 twWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlr 460
                                                  twWqtetGgi+itpl+g a+++kpgsat+P+fGi+++vvd  g  +e  +e g Lvi ++wP+++r
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 410 TWWQTETGGIMITPLAG-AIDAKPGSATKPFFGIRPAVVDAGGAVLEGATE-GNLVIADSWPGQMR 473
                                                  *****************.6***************************97777.79************ PP

                                    TIGR02188 461 tiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvshea 526
                                                  t+ygd++rfvetYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalvsh++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 474 TVYGDHQRFVETYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPK 539
                                                  ****************************************************************** PP

                                    TIGR02188 527 vaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktR 592
                                                  vaeaavvg p+eikg+ i+a+v+l +g++ ++ el+kel ++vrkeigpia+pd +++++ lPktR
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 540 VAEAAVVGCPHEIKGQGIYAYVTLIAGEQGSD-ELRKELVAWVRKEIGPIATPDYLQWAPGLPKTR 604
                                                  *****************************999.5******************************** PP

                                    TIGR02188 593 sGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                  sGkimRR+lrki e++ ++lgd+stl+dpsvv++l e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 605 SGKIMRRILRKIGENQpDQLGDISTLADPSVVKNLVE 641
                                                  *********************************9976 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.34
//
[ok]

This GapMind analysis is from Sep 17 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