GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium etli CFN 42

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_011427293.1 RHE_RS21025 acetate--CoA ligase

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



>NCBI__GCF_000092045.1:WP_011427293.1
          Length = 651

 Score =  883 bits (2282), Expect = 0.0
 Identities = 427/648 (65%), Positives = 497/648 (76%), Gaps = 3/648 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           ++PV  +V A  L D+  Y   Y++SV NPD FW +  KR+DW KP+T VK TSF    V
Sbjct: 5   IHPVPKQVKAQALIDKEKYLKWYEESVENPDKFWGKHGKRIDWFKPYTKVKNTSFTGK-V 63

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
            IKWF DG  NVSYNC+DRHL   GDQ+AIIWEGD+P   + ITY EL+E VC+ AN L+
Sbjct: 64  SIKWFEDGQTNVSYNCIDRHLKTNGDQVAIIWEGDNPYIDKKITYNELYEHVCRMANVLK 123

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
              V +GD VTIYMPMIPEA  AMLAC RIGA+HSVVFGGFSPEALAGRI+DC+S  VIT
Sbjct: 124 KHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPEALAGRIVDCESTFVIT 183

Query: 186 ADEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
            DEGVR GK +PLK N D A+     +  ++ KV+V +RT G   W   RD+WY   +  
Sbjct: 184 CDEGVRGGKPVPLKDNTDTAIHIAARQHVNVSKVLVVRRTGGKTGWAPGRDLWYHQEVAT 243

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P +M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++THE VFDY  G++YWC
Sbjct: 244 VKAECPPVKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYHHGDIYWC 303

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPL+N ATTL+FEGVPN+PD  R  +VIDKHKV+I YTAPTAIR+
Sbjct: 304 TADVGWVTGHSYIVYGPLSNCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRS 363

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M +G   V  +  SSLRLLG+VGEPINPEAW+WYY  VG +RCP++DTWWQTETGG +I
Sbjct: 364 LMGAGDDFVTRSSRSSLRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMI 423

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           +PLPGA  LKPGSAT PFFGV P LVDN G ++EGAA+GNL I DSWPGQ RT+YGDH+R
Sbjct: 424 TPLPGAIDLKPGSATVPFFGVKPELVDNEGKVLEGAADGNLCIADSWPGQMRTVYGDHER 483

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
           F+ TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+V+H  V+
Sbjct: 484 FIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVS 543

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PH IKGQGIY YVTL AG E ++ LR EL   VR EIGPIASPD IQ+APGLP
Sbjct: 544 EAAVVGYPHAIKGQGIYCYVTLMAGHEGTDTLRQELVKHVRAEIGPIASPDKIQFAPGLP 603

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           KTRSGKIMRRILRKIA  ++  LGD STLADP VV  LI   +    A
Sbjct: 604 KTRSGKIMRRILRKIAEDDFGALGDTSTLADPAVVDDLIANRQNKATA 651


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: 1448
Number of extensions: 67
Number of successful extensions: 4
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: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space:   375769
Effective search space used:   375769
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_011427293.1 RHE_RS21025 (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.1600521.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 1038.3   0.1          0 1038.1   0.1    1.0  1  NCBI__GCF_000092045.1:WP_011427293.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_011427293.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1038.1   0.1         0         0       3     628 ..      19     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1038.1 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           + e+y ++yee++e+p+kfw+k++k +++w+kp++kv+++s++   ++kWfedg++nvsync+drh++++ d+
  NCBI__GCF_000092045.1:WP_011427293.1  19 DKEKYLKWYEESVENPDKFWGKHGK-RIDWFKPYTKVKNTSFTGkvSIKWFEDGQTNVSYNCIDRHLKTNGDQ 90 
                                           6789*********************.5**************9887799************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vaiiwegd++    +k+tY+el+++vcr+anvlk++Gvkkgdrv+iY+pmipea++amlacaRiGavhsvvf+
  NCBI__GCF_000092045.1:WP_011427293.1  91 VAIIWEGDNPYI-DKKITYNELYEHVCRMANVLKKHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFG 162
                                           ********9996.9*********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216
                                           Gfs+eala Rivd+e+ +vit deg+Rggk ++lk+++d a++ a +   +v+kvlvv+rtg + + w  grD
  NCBI__GCF_000092045.1:WP_011427293.1 163 GFSPEALAGRIVDCESTFVITCDEGVRGGKPVPLKDNTDTAIHIAARqhvNVSKVLVVRRTGGK-TGWAPGRD 234
                                           *****************************************98765555799************.56****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +w++++v++ ++aec+p k+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++++di+wCtaD
  NCBI__GCF_000092045.1:WP_011427293.1 235 LWYHQEVAT-VKAECPPVKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYHHGDIYWCTAD 306
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGWvtGhsYivygPL+n attl+fegvp++pd++rfwevi+k+kv+ifYtaPtaiR+lm +g+++v++ ++ss
  NCBI__GCF_000092045.1:WP_011427293.1 307 VGWVTGHSYIVYGPLSNCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGAGDDFVTRSSRSS 379
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lg+vGepinpeaweWyy+vvG+++cp++dtwWqtetGg++itplpg a++lkpgsat+P+fG+++e+vd+
  NCBI__GCF_000092045.1:WP_011427293.1 380 LRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLPG-AIDLKPGSATVPFFGVKPELVDN 451
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           egk +e  ++ g L+i ++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvs
  NCBI__GCF_000092045.1:WP_011427293.1 452 EGKVLEGAAD-GNLCIADSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVS 523
                                           *****98777.79************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghrlgtae+esalvsh+ v+eaavvg+p+ ikg+ i+++v+l++g+e ++ +l++el k+vr+eigpia+pdk
  NCBI__GCF_000092045.1:WP_011427293.1 524 GHRLGTAEVESALVSHNLVSEAAVVGYPHAIKGQGIYCYVTLMAGHEGTD-TLRQELVKHVRAEIGPIASPDK 595
                                           ***********************************************999.5********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i++++ lPktRsGkimRR+lrkiae++  +lgd+stl+dp+vv++l++
  NCBI__GCF_000092045.1:WP_011427293.1 596 IQFAPGLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPAVVDDLIA 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 34.14
//
[ok]

This GapMind analysis is from Apr 09 2024. 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