GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingomonas histidinilytica UM2

Align Acetyl-coenzyme A synthetase 1; AcCoA synthetase 1; Acs 1; EC 6.2.1.1; Acetate--CoA ligase 1; Acyl-activating enzyme 1 (uncharacterized)
to candidate WP_079651098.1 B5X82_RS25170 acetate--CoA ligase

Query= curated2:Q88EH6
         (653 letters)



>NCBI__GCF_900167915.1:WP_079651098.1
          Length = 498

 Score =  662 bits (1707), Expect = 0.0
 Identities = 307/497 (61%), Positives = 386/497 (77%), Gaps = 3/497 (0%)

Query: 6   LYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSFDDHHV 65
           LYPV  E AA     +A YKA+Y +S+ +   FW EQA+R+DW++  T+  ++SFD+   
Sbjct: 4   LYPVPAEWAARAKVTDADYKALYARSIDDAHAFWLEQAKRLDWVRFPTRTNESSFDEADF 63

Query: 66  DIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEH-RNITYRELHEQVCKFANAL 124
            +KWFADG +NV++NCLDRHL ERGDQ+AIIWE D P++  R  TY+++HE+VC+FAN L
Sbjct: 64  QVKWFADGQINVAANCLDRHLAERGDQVAIIWEPDAPTDAPRRFTYKQVHEEVCRFANVL 123

Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184
           + Q V +GD VT+Y+PMIPEA  A+LACARIGAIHSVVFGGFSPEALAGRI DC S +VI
Sbjct: 124 KAQGVKKGDRVTVYLPMIPEAAFALLACARIGAIHSVVFGGFSPEALAGRIQDCDSSIVI 183

Query: 185 TADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDLMKVA 244
           TAD G RGG+  PLK NVD A  +    S++ +IV + TG ++     RDIWY++  K  
Sbjct: 184 TADCGRRGGKLVPLKTNVDAAAQH--APSLKSVIVIRATGSEVPMQAGRDIWYDEAAKNV 241

Query: 245 SSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEVYWCT 304
            + C  + M AE+ LFILYTSGSTGKPKGVLHTTGGYL++A+LTHE  FDYRPG+VYWC 
Sbjct: 242 PADCPAETMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLWASLTHEVCFDYRPGQVYWCA 301

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTAIRAM 364
           AD+GWVTGHSYIVYGPLANGATTL++EGVPN+PD +R+ ++VD+H+V I++TAPTA+RA+
Sbjct: 302 ADIGWVTGHSYIVYGPLANGATTLMYEGVPNWPDASRIWQVVDRHQVEIVFTAPTALRAL 361

Query: 365 MAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGGILIS 424
           M +G   V      SL+LLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETG  +I+
Sbjct: 362 MRDGDEFVARTSRKSLKLLGTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGAAMIA 421

Query: 425 PLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGDHDRF 484
           PLPGAT LKPGSATRP FGVVP LVD  G +++GA +GNL I  SWPGQ R+++GDH RF
Sbjct: 422 PLPGATDLKPGSATRPLFGVVPELVDADGKVLEGATDGNLCITRSWPGQMRTVWGDHARF 481

Query: 485 VDTYFKTFRGMYFTGDG 501
             TYF T+ G YFTGDG
Sbjct: 482 FQTYFSTYPGKYFTGDG 498


Lambda     K      H
   0.319    0.136    0.423 

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: 1097
Number of extensions: 65
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: 653
Length of database: 498
Length adjustment: 36
Effective length of query: 617
Effective length of database: 462
Effective search space:   285054
Effective search space used:   285054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_079651098.1 B5X82_RS25170 (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.2838469.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-228  746.4   0.0   1.3e-228  746.2   0.0    1.0  1  NCBI__GCF_900167915.1:WP_079651098.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079651098.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.2   0.0  1.3e-228  1.3e-228       5     486 ..      20     498 .]      16     498 .] 0.98

  Alignments for each domain:
  == domain 1  score: 746.2 bits;  conditional E-value: 1.3e-228
                             TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                            +yk+ly+++i+d ++fw ++ak+ l+w++  +++ ++s+++   +vkWf+dg++nv++nc+drh+++r d+v
  NCBI__GCF_900167915.1:WP_079651098.1  20 ADYKALYARSIDDAHAFWLEQAKR-LDWVRFPTRTNESSFDEadfQVKWFADGQINVAANCLDRHLAERGDQV 91 
                                           68*********************5.***********9999888889*************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           aiiwe d +++  r++tY+++++evcr+anvlk++Gvkkgdrv++Ylpmipea++a+lacaRiGa+hsvvf+G
  NCBI__GCF_900167915.1:WP_079651098.1  92 AIIWEPDAPTDAPRRFTYKQVHEEVCRFANVLKAQGVKKGDRVTVYLPMIPEAAFALLACARIGAIHSVVFGG 164
                                           **********99************************************************************* PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs+eala Ri+d+++ +vitad g Rggk ++lk++vd+a ++a+ s+++v+v++ tg+ev  ++ grD+w++
  NCBI__GCF_900167915.1:WP_079651098.1 165 FSPEALAGRIQDCDSSIVITADCGRRGGKLVPLKTNVDAAAQHAP-SLKSVIVIRATGSEVP-MQAGRDIWYD 235
                                           ********************************************9.7*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e+ + +++a+c++e++d+edplfiLYtsGstGkPkGvlhttgGyll+a+lt+++ fd+++++++wC+aD+GWv
  NCBI__GCF_900167915.1:WP_079651098.1 236 EAAK-NVPADCPAETMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLWASLTHEVCFDYRPGQVYWCAADIGWV 307
                                           **99.5******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivygPLanGattl++egvp++pdasr+w+v+++++v+i +taPta+Ralm+ g+e+v++++++sl++l
  NCBI__GCF_900167915.1:WP_079651098.1 308 TGHSYIVYGPLANGATTLMYEGVPNWPDASRIWQVVDRHQVEIVFTAPTALRALMRDGDEFVARTSRKSLKLL 380
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepinpeaw+Wy+evvG+++cpi+dtwWqtetG+++i+plpg at+lkpgsat+PlfG+ +e+vd +gk 
  NCBI__GCF_900167915.1:WP_079651098.1 381 GTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGAAMIAPLPG-ATDLKPGSATRPLFGVVPELVDADGKV 452
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDg 486
                                           +e  ++ g L+i+++wP+++rt++gd+ rf++tYf++++g yftGDg
  NCBI__GCF_900167915.1:WP_079651098.1 453 LEGATD-GNLCITRSWPGQMRTVWGDHARFFQTYFSTYPGKYFTGDG 498
                                           *98777.79*************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (498 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.46
//
[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