GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium grahamii CCGE 502

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_016556836.1 RGCCGE502_RS24205 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000298315.2:WP_016556836.1
          Length = 651

 Score =  887 bits (2291), Expect = 0.0
 Identities = 421/639 (65%), Positives = 505/639 (79%), Gaps = 9/639 (1%)

Query: 13  IADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYED 72
           + +  LI+  +YE  Y++S+  PD FWG+ GK +DW KPY KVKNTSF  G VSIKW+ED
Sbjct: 12  VKNHALIDKAKYEQWYEESVENPDKFWGKHGKRIDWFKPYTKVKNTSFT-GRVSIKWFED 70

Query: 73  GTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKG 132
           G  N++ NC+DRHL+ NG++TAII+EGD+    K I+Y EL+  VCR AN + + G+KKG
Sbjct: 71  GQTNVSYNCIDRHLKTNGNQTAIIFEGDNPYVDKKITYNELYEHVCRMANVMKKHGVKKG 130

Query: 133 DVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRA 192
           D V IYMPM+PEAA AMLACARIGAVHSV+FGGFSPEA+AGRI+D  S  V+T DEGVR 
Sbjct: 131 DRVTIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPEALAGRIVDCESTFVVTCDEGVRG 190

Query: 193 GRSIPLKKNVDDALKNPNVTSVEHVVV-----LKRTGGKIDWQEGRDLWWHDLVEQASDQ 247
           G+ +PLK N D A+   ++ + +HV+V     ++RTGGK  W  GRDLW+H  +     +
Sbjct: 191 GKPVPLKDNTDTAI---HIAARQHVIVDKVLVVRRTGGKTGWAPGRDLWYHQEIATVKPE 247

Query: 248 HQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADV 307
               +M AEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA+T +YVFDYHPGDIYWCTADV
Sbjct: 248 CPPVKMRAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTHEYVFDYHPGDIYWCTADV 307

Query: 308 GWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAE 367
           GWVTGHSY++YGPLA  ATTLMFEGVPN+P   R  +V+DKH+VNI YTAPTAIR+LM  
Sbjct: 308 GWVTGHSYIVYGPLANCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGA 367

Query: 368 GDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLP 427
           GD  +  + RSSLR+LG+VGEPINPEAWEWY+  +G+++CPV+DTWWQTETGG MITPLP
Sbjct: 368 GDHFVTRSSRSSLRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLP 427

Query: 428 GATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQT 487
           GAT+LK GSAT PFFGV+P LVDNEGN L+GA +G+L I DSWPGQ RT++GDHERF QT
Sbjct: 428 GATDLKPGSATTPFFGVKPQLVDNEGNVLQGAADGNLCIIDSWPGQMRTVYGDHERFIQT 487

Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547
           YFST+K  YF+GDG RRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H  ++EAAV
Sbjct: 488 YFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSEAAV 547

Query: 548 VGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607
           VG PH IKGQ IY YVTL  G E S +L  ++   VR EIGP+A PD + +   LPKTRS
Sbjct: 548 VGYPHPIKGQGIYCYVTLMAGNEGSDDLRQQLVKHVRSEIGPIAAPDKIQFAPGLPKTRS 607

Query: 608 GKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           GKIMRRILRKIA  D  +LGDTSTLADP VV+ L+  +Q
Sbjct: 608 GKIMRRILRKIAEDDFGSLGDTSTLADPAVVDDLIANRQ 646


Lambda     K      H
   0.317    0.135    0.421 

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: 1499
Number of extensions: 55
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: 652
Length of database: 651
Length adjustment: 38
Effective length of query: 614
Effective length of database: 613
Effective search space:   376382
Effective search space used:   376382
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 WP_016556836.1 RGCCGE502_RS24205 (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.2457888.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 1033.8   0.0          0 1033.6   0.0    1.0  1  NCBI__GCF_000298315.2:WP_016556836.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000298315.2:WP_016556836.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1033.6   0.0         0         0       4     628 ..      20     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1033.6 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                             +y+++yee++e+p+kfw+k++k +++w+kp++kv+++s++   ++kWfedg++nvsync+drh++++ +++
  NCBI__GCF_000298315.2:WP_016556836.1  20 KAKYEQWYEESVENPDKFWGKHGK-RIDWFKPYTKVKNTSFTGrvSIKWFEDGQTNVSYNCIDRHLKTNGNQT 91 
                                           679*********************.5**************998789*************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           aii+egd++    +k+tY+el+++vcr+anv+k++Gvkkgdrv+iY+pmipea++amlacaRiGavhsvvf+G
  NCBI__GCF_000298315.2:WP_016556836.1  92 AIIFEGDNPYV-DKKITYNELYEHVCRMANVMKKHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFGG 163
                                           *******9996.9************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrDv 217
                                           fs+eala Rivd+e+ +v+t deg+Rggk ++lk+++d a++ a +    v+kvlvv+rtg + + w  grD+
  NCBI__GCF_000298315.2:WP_016556836.1 164 FSPEALAGRIVDCESTFVVTCDEGVRGGKPVPLKDNTDTAIHIAARqhvIVDKVLVVRRTGGK-TGWAPGRDL 235
                                           ****************************************98766545689************.56******* PP

                             TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290
                                           w+++++++ ++ ec+p k+ +edplfiLYtsGstGkPkGvlhttgGyl++aa+t++yvfd++++di+wCtaDv
  NCBI__GCF_000298315.2:WP_016556836.1 236 WYHQEIAT-VKPECPPVKMRAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTHEYVFDYHPGDIYWCTADV 307
                                           *******6.**************************************************************** PP

                             TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363
                                           GWvtGhsYivygPLan attl+fegvp++pd++rfwevi+k+kv+ifYtaPtaiR+lm +g+++v++ ++ssl
  NCBI__GCF_000298315.2:WP_016556836.1 308 GWVTGHSYIVYGPLANCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGAGDHFVTRSSRSSL 380
                                           ************************************************************************* PP

                             TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436
                                           r+lg+vGepinpeaweWyy+vvG+++cp++dtwWqtetGg++itplpg at+lkpgsat+P+fG+++++vd+e
  NCBI__GCF_000298315.2:WP_016556836.1 381 RLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLPG-ATDLKPGSATTPFFGVKPQLVDNE 452
                                           ************************************************.6*********************** PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           g+ ++  ++ g L+i ++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvsG
  NCBI__GCF_000298315.2:WP_016556836.1 453 GNVLQGAAD-GNLCIIDSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSG 524
                                           ****98777.79************************************************************* PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           hrlgtae+esalvsh+ v+eaavvg+p+ ikg+ i+++v+l++g+e +++ l+++l k+vr+eigpia+pdki
  NCBI__GCF_000298315.2:WP_016556836.1 525 HRLGTAEVESALVSHNLVSEAAVVGYPHPIKGQGIYCYVTLMAGNEGSDD-LRQQLVKHVRSEIGPIAAPDKI 596
                                           **********************************************9995.********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++++ lPktRsGkimRR+lrkiae++  +lgd+stl+dp+vv++l++
  NCBI__GCF_000298315.2:WP_016556836.1 597 QFAPGLPKTRSGKIMRRILRKIAEDDfGSLGDTSTLADPAVVDDLIA 643
                                           *******************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (651 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: 25.18
//
[ok]

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

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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