GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Sphingomonas koreensis DSMZ 15582

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Ga0059261_1313 Ga0059261_1313 acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>lcl|FitnessBrowser__Korea:Ga0059261_1313 Ga0059261_1313
           acetyl-coenzyme A synthetase (EC 6.2.1.1)
          Length = 645

 Score =  882 bits (2279), Expect = 0.0
 Identities = 422/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           ++PV  E A     D A Y+ +Y +S+ +P  FW +QAKRLDW+K        SFD+   
Sbjct: 5   IHPVPAEWAREARYDAAGYEQLYGRSIADPGSFWLDQAKRLDWVKRPELAGDWSFDESDF 64

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFANAL 124
            I+WFADG LNV+ NC+DRHLA RGD++AIIWE DDP+E SR  TYRELHEEVC+FAN L
Sbjct: 65  RIEWFADGKLNVAANCIDRHLASRGDEVAIIWEPDDPAEASRQFTYRELHEEVCRFANVL 124

Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184
           +GQ V +GD VTIYMPMIPEA  A+LAC R+GAIHSVVFGGFSPEALAGRI DC S VVI
Sbjct: 125 KGQGVKKGDRVTIYMPMIPEAAFAILACARLGAIHSVVFGGFSPEALAGRITDCDSSVVI 184

Query: 185 TADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
           TADEG R GK+I LKANVD A       +++KVIV K T G++     RD+WY +     
Sbjct: 185 TADEGRRGGKRIALKANVDAAAER--APALEKVIVVKATGGHVTMTPGRDVWYHEAAAGV 242

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
           GT C  + M AE+ LFILYTSGSTGKPKGV HT+AGYLL+A+LTHE  FDY+PG V+WC 
Sbjct: 243 GTDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFDYRPGNVWWCA 302

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           AD+GWVTGHSYI+YGPLANGATTL++EG+PN+PD +R+ +V+D+H V  ++TAPTA+RA+
Sbjct: 303 ADIGWVTGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRAL 362

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           M  G   V     +SLRLLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETGG +I+
Sbjct: 363 MKDGDDFVTKTSRTSLRLLGTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIA 422

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           P+PGAT LKPGSATRP  GV P LVD+ G ++ GA EGNLVI  SWPGQ RT++GDH+RF
Sbjct: 423 PMPGATDLKPGSATRPLPGVDPQLVDSEGAVLHGATEGNLVIARSWPGQMRTVWGDHERF 482

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
             TYF T+ G YFTGDG RRDEDGYYWITGRVDDV+NVSGHRMGTAE+ESA+V HPKVAE
Sbjct: 483 FQTYFTTYPGKYFTGDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAE 542

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           AAVVG+PHD+KGQGIY YVTLNAG    +ALR EL  WVR EIGPIA+PD +Q+APGLPK
Sbjct: 543 AAVVGMPHDVKGQGIYAYVTLNAGCAADDALRAELVKWVRTEIGPIATPDALQFAPGLPK 602

Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA  +   LGD STLADP VV  L+
Sbjct: 603 TRSGKIMRRILRKIAEGDVSSLGDTSTLADPSVVDDLV 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: 1489
Number of extensions: 68
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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 Ga0059261_1313 Ga0059261_1313 (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.11566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-301  985.3   0.0   6.6e-301  985.0   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1313  Ga0059261_1313 acetyl-coenzyme A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1313  Ga0059261_1313 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 !  985.0   0.0  6.6e-301  6.6e-301       5     627 ..      21     640 ..      18     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 985.0 bits;  conditional E-value: 6.6e-301
                                 TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekr 70 
                                                 y++ly ++i+dp +fw ++ak+ l+w+k  e   d+s+++   +++Wf+dg+lnv++nc+drh+++r
  lcl|FitnessBrowser__Korea:Ga0059261_1313  21 AGYEQLYGRSIADPGSFWLDQAKR-LDWVKRPELAGDWSFDEsdfRIEWFADGKLNVAANCIDRHLASR 88 
                                               579********************5.**************99888899********************** PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                                d+vaiiwe d++ e sr++tY+el++evcr+anvlk +Gvkkgdrv+iY+pmipea++a+lacaR+Ga
  lcl|FitnessBrowser__Korea:Ga0059261_1313  89 GDEVAIIWEPDDPAEASRQFTYRELHEEVCRFANVLKGQGVKKGDRVTIYMPMIPEAAFAILACARLGA 157
                                               ********************************************************************* PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208
                                               +hsvvf+Gfs+eala Ri+d+++ +vitadeg Rggk+i+lk++vd+a e+a+ ++ekv+vvk tg +v
  lcl|FitnessBrowser__Korea:Ga0059261_1313 158 IHSVVFGGFSPEALAGRITDCDSSVVITADEGRRGGKRIALKANVDAAAERAP-ALEKVIVVKATGGHV 225
                                               ****************************************************9.7*************7 PP

                                 TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
                                               + ++ grDvw++e+ + ++ ++c++e++++edplfiLYtsGstGkPkGvlht++Gyll+a+lt+++ fd
  lcl|FitnessBrowser__Korea:Ga0059261_1313 226 T-MTPGRDVWYHEAAA-GVGTDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFD 292
                                               6.**************.6*************************************************** PP

                                 TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346
                                               +++++++wC+aD+GWvtGhsYi+ygPLanGattl++eg p++pdasr+w+v+++++v + +taPta+Ra
  lcl|FitnessBrowser__Korea:Ga0059261_1313 293 YRPGNVWWCAADIGWVTGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRA 361
                                               ********************************************************************* PP

                                 TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
                                               lmk g+++v+k+++ slr+lg+vGepinpeaw+Wy+evvG+++cpi+dtwWqtetGg++i+p+pg at+
  lcl|FitnessBrowser__Korea:Ga0059261_1313 362 LMKDGDDFVTKTSRTSLRLLGTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIAPMPG-ATD 429
                                               *****************************************************************.6** PP

                                 TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484
                                               lkpgsat+Pl+G+++++vd+eg  ++  +e g Lvi ++wP+++rt++gd+erf++tYf++++g yftG
  lcl|FitnessBrowser__Korea:Ga0059261_1313 430 LKPGSATRPLPGVDPQLVDSEGAVLHGATE-GNLVIARSWPGQMRTVWGDHERFFQTYFTTYPGKYFTG 497
                                               *************************97777.79************************************ PP

                                 TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553
                                               Dg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv h++vaeaavvg+p+++kg+ i+a+v+l++g
  lcl|FitnessBrowser__Korea:Ga0059261_1313 498 DGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAEAAVVGMPHDVKGQGIYAYVTLNAG 566
                                               ********************************************************************* PP

                                 TIGR02188 554 veedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621
                                                ++d+ +l++el k+vr+eigpia+pd +++++ lPktRsGkimRR+lrkiaeg+ ++lgd+stl+dps
  lcl|FitnessBrowser__Korea:Ga0059261_1313 567 CAADD-ALRAELVKWVRTEIGPIATPDALQFAPGLPKTRSGKIMRRILRKIAEGDvSSLGDTSTLADPS 634
                                               **999.5************************************************************** PP

                                 TIGR02188 622 vveelk 627
                                               vv++l 
  lcl|FitnessBrowser__Korea:Ga0059261_1313 635 VVDDLV 640
                                               **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.80
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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