GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhodobacter maris JA276

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_097068839.1 CRO22_RS01345 acetate--CoA ligase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>NCBI__GCF_900217815.1:WP_097068839.1
          Length = 644

 Score =  828 bits (2140), Expect = 0.0
 Identities = 409/631 (64%), Positives = 477/631 (75%), Gaps = 5/631 (0%)

Query: 16  NTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTL 75
           N   +   Y  MY++S+ NPD FW  + KRLDW+ P+T VK T F    V IKWF DG L
Sbjct: 10  NAHANNQKYLEMYRESIENPDAFWGREGKRLDWMTPYTKVKNTDFTFGKVSIKWFEDGVL 69

Query: 76  NVSYNCLDRHLAERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQDVHRGDV 134
           N S NC+DRHL +R  Q AII+E DDP+E +++ITY+EL E+V + AN L  Q + RGD 
Sbjct: 70  NASVNCIDRHLRDRALQTAIIFEPDDPSEPAQHITYKELSEKVNRMANVLLSQGIMRGDR 129

Query: 135 VTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGLRAGK 194
           V IY+PMIPEA  AMLAC RIGAIHS+VF GFSP+ALA RI DC +K+VITAD   R G+
Sbjct: 130 VVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPDALANRINDCGAKLVITADTAPRGGR 189

Query: 195 KISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGTVCAPKEMG 254
           +  LKAN D AL +   S   + +V KRTG  I W   RD+    LM+     C P+ M 
Sbjct: 190 RTPLKANTDAALLH--CSDKVRCLVVKRTGDQISWVHGRDVDLLYLMEHVSPECPPRPMN 247

Query: 255 AEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTADVGWVTGHT 314
           AE+ LFILYTSGSTGKPKGV HTTGGYL YAA+TH+  FDY+ G+++WCTADVGWVTGH+
Sbjct: 248 AEDPLFILYTSGSTGKPKGVVHTTGGYLCYAAMTHQYTFDYQDGDVFWCTADVGWVTGHS 307

Query: 315 YIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMAQGTAAVEG 374
           YI+YGPLANGATTL+FEGVP YPD  R   + +KHKVN  YTAPTAIRA+M QGT  VE 
Sbjct: 308 YIIYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRALMGQGTEWVEK 367

Query: 375 ADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPLPGAHGLKP 434
            D SSL++LGSVGEPINPEAW WY K++G+ +CPIVDT+WQTETG  +++PLPGA   KP
Sbjct: 368 YDLSSLKVLGSVGEPINPEAWVWYDKHIGKGKCPIVDTFWQTETGGHMITPLPGATPTKP 427

Query: 435 GSAARPFFGVVPALVD--NLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTF 492
           GSA  PFFGV P ++D      I E   EG L I DSWPGQ RT++GDHDRF +TYF  +
Sbjct: 428 GSATNPFFGVKPVVLDPQTAVRIGEVECEGVLCISDSWPGQMRTVWGDHDRFQETYFGQY 487

Query: 493 RGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPH 552
           RG YFTGDG RRD DGY+WITGRVDDV+NVSGHRMGTAE+ESA+VAH +VAEAAVVG PH
Sbjct: 488 RGYYFTGDGCRRDKDGYYWITGRVDDVINVSGHRMGTAEVESALVAHQQVAEAAVVGYPH 547

Query: 553 DIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMR 612
           DIKGQGIY YVTL  G EPSE LR +L  WVR EIGPIASPD+IQWAPGLPKTRSGKIMR
Sbjct: 548 DIKGQGIYAYVTLMNGVEPSEELRKDLVKWVRTEIGPIASPDLIQWAPGLPKTRSGKIMR 607

Query: 613 RILRKIATGEYDGLGDISTLADPGVVQHLID 643
           RILRKIA  +Y  LGDISTLADP VVQ LID
Sbjct: 608 RILRKIAENDYGALGDISTLADPSVVQELID 638


Lambda     K      H
   0.319    0.136    0.425 

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: 1430
Number of extensions: 59
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: 644
Length adjustment: 38
Effective length of query: 613
Effective length of database: 606
Effective search space:   371478
Effective search space used:   371478
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: 54 (25.4 bits)

Align candidate WP_097068839.1 CRO22_RS01345 (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.3010808.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 1027.2   0.0          0 1027.0   0.0    1.0  1  NCBI__GCF_900217815.1:WP_097068839.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900217815.1:WP_097068839.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1027.0   0.0         0         0       3     628 ..      14     638 ..      12     639 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1027.0 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           ++++y e+y+e+ie+p++fw++++k +l+w++p++kv++++++    ++kWfedg ln+s+nc+drh+++r+ 
  NCBI__GCF_900217815.1:WP_097068839.1  14 NNQKYLEMYRESIENPDAFWGREGK-RLDWMTPYTKVKNTDFTFgkvSIKWFEDGVLNASVNCIDRHLRDRAL 85 
                                           7899*********************.5**************9877789************************* PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           ++aii+e d+++e ++++tY+el ++v+r+anvl ++G+ +gdrv+iYlpmipea++amlacaRiGa+hs+vf
  NCBI__GCF_900217815.1:WP_097068839.1  86 QTAIIFEPDDPSEPAQHITYKELSEKVNRMANVLLSQGIMRGDRVVIYLPMIPEAAYAMLACARIGAIHSIVF 158
                                           ************************************************************************* PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvw 218
                                           aGfs++ala+Ri+d+ aklvitad++ Rgg++++lk+++d+al +++++v+ +lvvkrtg++++ w++grDv 
  NCBI__GCF_900217815.1:WP_097068839.1 159 AGFSPDALANRINDCGAKLVITADTAPRGGRRTPLKANTDAALLHCSDKVR-CLVVKRTGDQIS-WVHGRDVD 229
                                           ***********************************************9997.9*********76.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           +  l+e+ +s ec+p+++++edplfiLYtsGstGkPkGv+httgGyl +aa+t++y+fd++d+d+fwCtaDvG
  NCBI__GCF_900217815.1:WP_097068839.1 230 LLYLMEH-VSPECPPRPMNAEDPLFILYTSGSTGKPKGVVHTTGGYLCYAAMTHQYTFDYQDGDVFWCTADVG 301
                                           ******6.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsYi+ygPLanGattl+fegvptypda+rfw+v+ek+kv++fYtaPtaiRalm +g+e+v+k+dlssl+
  NCBI__GCF_900217815.1:WP_097068839.1 302 WVTGHSYIIYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRALMGQGTEWVEKYDLSSLK 374
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.ee 436
                                           vlgsvGepinpeaw Wy +++Gk+kcpivdt+WqtetGg++itplpg at++kpgsat+P+fG++++v+d ++
  NCBI__GCF_900217815.1:WP_097068839.1 375 VLGSVGEPINPEAWVWYDKHIGKGKCPIVDTFWQTETGGHMITPLPG-ATPTKPGSATNPFFGVKPVVLDpQT 446
                                           ***********************************************.6*********************666 PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           + ++ e e +gvL+i+++wP+++rt++gd++rf+etYf +++g+yftGDg+rrdkdGy+wi+GRvDdvinvsG
  NCBI__GCF_900217815.1:WP_097068839.1 447 AVRIGEVECEGVLCISDSWPGQMRTVWGDHDRFQETYFGQYRGYYFTGDGCRRDKDGYYWITGRVDDVINVSG 519
                                           6667799999*************************************************************** PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           hr+gtae+esalv+h++vaeaavvg+p++ikg+ i+a+v+l++gve++ee l+k+l k+vr+eigpia+pd i
  NCBI__GCF_900217815.1:WP_097068839.1 520 HRMGTAEVESALVAHQQVAEAAVVGYPHDIKGQGIYAYVTLMNGVEPSEE-LRKDLVKWVRTEIGPIASPDLI 591
                                           *************************************************5.********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++++ lPktRsGkimRR+lrkiae++  +lgd+stl+dpsvv+el++
  NCBI__GCF_900217815.1:WP_097068839.1 592 QWAPGLPKTRSGKIMRRILRKIAENDyGALGDISTLADPSVVQELID 638
                                           **************************99***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (644 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: 18.99
//
[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