GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingomonas histidinilytica UM2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_079651030.1 B5X82_RS24705 acetate--CoA ligase

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



>NCBI__GCF_900167915.1:WP_079651030.1
          Length = 499

 Score =  629 bits (1623), Expect = 0.0
 Identities = 300/500 (60%), Positives = 373/500 (74%), Gaps = 3/500 (0%)

Query: 3   AASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDD 62
           A +LYPV    AA +    A   A +  S+ +P+ +W ++A RLDW +  T   ++SFD+
Sbjct: 2   ADNLYPVPASWAAKSRMTAAERAADHGFSLASPERYWLDRAGRLDWFRFPTKADESSFDE 61

Query: 63  HHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSES-RNITYRELHEEVCKFA 121
               +KWFADG LNVS NC+DRHLAE GDQ+AI+WE DDP+E+ R  TY +LHEEVC+ A
Sbjct: 62  ADFQVKWFADGELNVSVNCIDRHLAEHGDQVAIVWEPDDPAEAPRRFTYAQLHEEVCRLA 121

Query: 122 NALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSK 181
           N L+   V +G  VTIY+PMIPEA  A+LAC RIGAIHSVVFGGFSP+ALAGRI DC S 
Sbjct: 122 NVLKAHGVKKGHRVTIYLPMIPEAAFALLACARIGAIHSVVFGGFSPDALAGRIQDCDSS 181

Query: 182 VVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLM 241
           VVITAD G R GK +PLKANVD+AL   + +S++ V+V + T G ++    RD+W ++ +
Sbjct: 182 VVITADHGRRGGKLVPLKANVDEALK--QCTSVETVVVVRATDGAVEMVPGRDVWLDEAI 239

Query: 242 KVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVY 301
           +     C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL+A+LTHE  FDY+ G+V+
Sbjct: 240 RHVAADCPPERMNAEDPLFILYTSGSTGKPKGVVHTTGGYLLWASLTHELCFDYRRGDVF 299

Query: 302 WCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAI 361
           WC+AD+GWVTGHSYIVYGPLANGATTL++EGVPN+P  +R+ +V+D+H V  L+TAPTA+
Sbjct: 300 WCSADIGWVTGHSYIVYGPLANGATTLIYEGVPNWPSPSRMWEVVDRHGVHTLFTAPTAL 359

Query: 362 RAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGV 421
           RA+M  G   V G    SLRLLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETG  
Sbjct: 360 RALMREGDDFVAGTSRKSLRLLGTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGAA 419

Query: 422 LISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDH 481
           +I+P+PGATALKPGSAT P  GV P LVD  G  +EG  EGNL I  SWPGQ RT++GDH
Sbjct: 420 MIAPMPGATALKPGSATLPMPGVAPELVDAEGRPVEGTGEGNLCIARSWPGQMRTVWGDH 479

Query: 482 DRFVDTYFKTFSGMYFTGDG 501
            RF  TYF T+ G YFTGDG
Sbjct: 480 ARFFQTYFSTYPGKYFTGDG 499


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: 1088
Number of extensions: 54
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: 499
Length adjustment: 36
Effective length of query: 615
Effective length of database: 463
Effective search space:   284745
Effective search space used:   284745
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: 53 (25.0 bits)

Align candidate WP_079651030.1 B5X82_RS24705 (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.2980803.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-226  736.9   0.0     1e-225  736.7   0.0    1.0  1  NCBI__GCF_900167915.1:WP_079651030.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079651030.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.7   0.0    1e-225    1e-225      13     486 ..      29     499 .]      18     499 .] 0.97

  Alignments for each domain:
  == domain 1  score: 736.7 bits;  conditional E-value: 1e-225
                             TIGR02188  13 eaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiwegde 82 
                                            + ++pe++w + a  +l+w++  +k  ++s+++   +vkWf+dgelnvs+nc+drh++++ d+vai+we d+
  NCBI__GCF_900167915.1:WP_079651030.1  29 FSLASPERYWLDRAG-RLDWFRFPTKADESSFDEadfQVKWFADGELNVSVNCIDRHLAEHGDQVAIVWEPDD 100
                                           567889********9.5**********99999887889*********************************** PP

                             TIGR02188  83 egedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealae 155
                                           + e  r++tYa+l++evcrlanvlk++Gvkkg rv+iYlpmipea++a+lacaRiGa+hsvvf+Gfs++ala 
  NCBI__GCF_900167915.1:WP_079651030.1 101 PAEAPRRFTYAQLHEEVCRLANVLKAHGVKKGHRVTIYLPMIPEAAFALLACARIGAIHSVVFGGFSPDALAG 173
                                           ************************************************************************* PP

                             TIGR02188 156 RivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekeas 228
                                           Ri+d+++ +vitad+g Rggk ++lk++vdeal++++ sve+v+vv+ t+  v+ ++ grDvw++e++++ + 
  NCBI__GCF_900167915.1:WP_079651030.1 174 RIQDCDSSVVITADHGRRGGKLVPLKANVDEALKQCT-SVETVVVVRATDGAVE-MVPGRDVWLDEAIRH-VA 243
                                           ************************************8.8*************66.**************6.** PP

                             TIGR02188 229 aecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivy 301
                                           a+c+pe++++edplfiLYtsGstGkPkGv+httgGyll+a+lt+++ fd++ +d+fwC+aD+GWvtGhsYivy
  NCBI__GCF_900167915.1:WP_079651030.1 244 ADCPPERMNAEDPLFILYTSGSTGKPKGVVHTTGGYLLWASLTHELCFDYRRGDVFWCSADIGWVTGHSYIVY 316
                                           ************************************************************************* PP

                             TIGR02188 302 gPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepin 374
                                           gPLanGattl++egvp++p++sr+wev+++++v +++taPta+Ralm++g+++v+ ++++slr+lg+vGepin
  NCBI__GCF_900167915.1:WP_079651030.1 317 GPLANGATTLIYEGVPNWPSPSRMWEVVDRHGVHTLFTAPTALRALMREGDDFVAGTSRKSLRLLGTVGEPIN 389
                                           ************************************************************************* PP

                             TIGR02188 375 peaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeegg 447
                                           peaw+Wy+evvG+++cpi+dtwWqtetG+++i+p+pg at+lkpgsatlP++G+ +e+vd eg++ve + e g
  NCBI__GCF_900167915.1:WP_079651030.1 390 PEAWRWYHEVVGEGRCPIIDTWWQTETGAAMIAPMPG-ATALKPGSATLPMPGVAPELVDAEGRPVEGTGE-G 460
                                           *************************************.6****************************7666.7 PP

                             TIGR02188 448 vLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDg 486
                                            L+i ++wP+++rt++gd+ rf++tYf++++g yftGDg
  NCBI__GCF_900167915.1:WP_079651030.1 461 NLCIARSWPGQMRTVWGDHARFFQTYFSTYPGKYFTGDG 499
                                           8*************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (499 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: 30.66
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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