Alignments for a candidate for acs in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1313
          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.2260136.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  FitnessBrowser__Korea:Ga0059261_1313  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Korea:Ga0059261_1313  
   #    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...kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                             y++ly ++i+dp +fw ++ak+ l+w+k  e   d+s+++   +++Wf+dg+lnv++nc+drh+++r d+v
  FitnessBrowser__Korea:Ga0059261_1313  21 AGYEQLYGRSIADPGSFWLDQAKR-LDWVKRPELAGDWSFDEsdfRIEWFADGKLNVAANCIDRHLASRGDEV 92 
                                           579********************5.**************99888899************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           aiiwe d++ e sr++tY+el++evcr+anvlk +Gvkkgdrv+iY+pmipea++a+lacaR+Ga+hsvvf+G
  FitnessBrowser__Korea:Ga0059261_1313  93 AIIWEPDDPAEASRQFTYRELHEEVCRFANVLKGQGVKKGDRVTIYMPMIPEAAFAILACARLGAIHSVVFGG 165
                                           ************************************************************************* PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs+eala Ri+d+++ +vitadeg Rggk+i+lk++vd+a e+a+ ++ekv+vvk tg +v+ ++ grDvw++
  FitnessBrowser__Korea:Ga0059261_1313 166 FSPEALAGRITDCDSSVVITADEGRRGGKRIALKANVDAAAERAP-ALEKVIVVKATGGHVT-MTPGRDVWYH 236
                                           ********************************************9.7*************76.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e+ + ++ ++c++e++++edplfiLYtsGstGkPkGvlht++Gyll+a+lt+++ fd+++++++wC+aD+GWv
  FitnessBrowser__Korea:Ga0059261_1313 237 EAAA-GVGTDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFDYRPGNVWWCAADIGWV 308
                                           ****.6******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYi+ygPLanGattl++eg p++pdasr+w+v+++++v + +taPta+Ralmk g+++v+k+++ slr+l
  FitnessBrowser__Korea:Ga0059261_1313 309 TGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRALMKDGDDFVTKTSRTSLRLL 381
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepinpeaw+Wy+evvG+++cpi+dtwWqtetGg++i+p+pg at+lkpgsat+Pl+G+++++vd+eg  
  FitnessBrowser__Korea:Ga0059261_1313 382 GTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIAPMPG-ATDLKPGSATRPLPGVDPQLVDSEGAV 453
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ++  +e g Lvi ++wP+++rt++gd+erf++tYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+
  FitnessBrowser__Korea:Ga0059261_1313 454 LHGATE-GNLVIARSWPGQMRTVWGDHERFFQTYFTTYPGKYFTGDGCRRDEDGYYWITGRVDDVINVSGHRM 525
                                           *97777.79**************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalv h++vaeaavvg+p+++kg+ i+a+v+l++g ++d+ +l++el k+vr+eigpia+pd ++++
  FitnessBrowser__Korea:Ga0059261_1313 526 GTAEVESALVLHPKVAEAAVVGMPHDVKGQGIYAYVTLNAGCAADD-ALRAELVKWVRTEIGPIATPDALQFA 597
                                           *******************************************999.5************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           + lPktRsGkimRR+lrkiaeg+ ++lgd+stl+dpsvv++l 
  FitnessBrowser__Korea:Ga0059261_1313 598 PGLPKTRSGKIMRRILRKIAEGDvSSLGDTSTLADPSVVDDLV 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 19.13
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources