GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Microvirga lotononidis WSM3557

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_009493644.1 MICLODRAFT_RS29080 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000262405.1:WP_009493644.1
          Length = 652

 Score =  914 bits (2363), Expect = 0.0
 Identities = 421/640 (65%), Positives = 517/640 (80%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           + +PA    R  ++   Y A Y+ S+  P+ FW E+ K +DW K   ++KNT+F P NV+
Sbjct: 6   YDVPAEWRHRAYLDDAGYRAKYEASVKDPEAFWAEEAKRIDWFKAPTRIKNTNFGPDNVA 65

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           I+W+EDG  N+A NC+DRHL   GD+ AIIWEGDD S+SK I+Y+ELH +VCR AN +  
Sbjct: 66  IRWFEDGVTNVAHNCIDRHLHTRGDQVAIIWEGDDPSESKKITYRELHDEVCRMANIMRN 125

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
            G+ KGD V IYMPM+PEAA AMLACAR+GA+HSV+FGGFSP+++A RI D+ S  ++T+
Sbjct: 126 RGVAKGDRVTIYMPMIPEAAYAMLACARLGAIHSVVFGGFSPDSLASRIQDAKSAFIVTA 185

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246
           DEG+R GR +PLK NVD AL+      V+HV+V++RTG  ++   GRD+++H+  E  SD
Sbjct: 186 DEGLRGGRKVPLKVNVDAALERVGAGVVDHVLVVRRTGSPVNMVPGRDVYYHEAAELVSD 245

Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306
           +   EEMNAEDPLFILYTSGSTG PKGVLHTTGGYLVYA++T +YVFDYH GD+YWCTAD
Sbjct: 246 ECPCEEMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYASMTHQYVFDYHDGDVYWCTAD 305

Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366
           VGWVTGHSY+LYGPLA GATTLMFEGVP +PT +R   V+DKHQVNI YTAPTAIR+LM 
Sbjct: 306 VGWVTGHSYILYGPLANGATTLMFEGVPTYPTISRFWDVIDKHQVNIFYTAPTAIRSLMQ 365

Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426
            G++ ++ T R SLR+LGSVGEPINPEAWEWY + +G+ +CP+VDTWWQTETGG +ITPL
Sbjct: 366 AGEEPVKKTSRKSLRLLGSVGEPINPEAWEWYHRVVGDGRCPIVDTWWQTETGGILITPL 425

Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486
           PGAT+LK GSATRPFFGV+P +VD +G  LEGATEG+LVI DSWPGQ RT++GDHERF Q
Sbjct: 426 PGATKLKPGSATRPFFGVKPQIVDADGKVLEGATEGNLVIADSWPGQMRTVYGDHERFVQ 485

Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546
           TYFST+   YF+GDG RRD+DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAHPK++EAA
Sbjct: 486 TYFSTYPGKYFTGDGCRRDQDGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVSEAA 545

Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606
           VVG PH+IKGQ IYAYVTL  GEEPS EL  E+  WVRKEIGP+A+PD++ +   LPKTR
Sbjct: 546 VVGYPHDIKGQGIYAYVTLMAGEEPSEELRKELVAWVRKEIGPIASPDLIQFAPGLPKTR 605

Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           SGKIMRRILRKIA  +  +LGDTSTLADPGVV+ L+  +Q
Sbjct: 606 SGKIMRRILRKIAEDEFGSLGDTSTLADPGVVDDLITNRQ 645


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: 1461
Number of extensions: 48
Number of successful extensions: 1
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: 652
Length adjustment: 38
Effective length of query: 614
Effective length of database: 614
Effective search space:   376996
Effective search space used:   376996
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_009493644.1 MICLODRAFT_RS29080 (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.1859544.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 1033.2   0.0          0 1032.8   0.0    1.0  1  NCBI__GCF_000262405.1:WP_009493644.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000262405.1:WP_009493644.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1032.8   0.0         0         0       6     628 ..      22     642 ..      18     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1032.8 bits;  conditional E-value: 0
                             TIGR02188   6 eykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                            y++ ye +++dpe+fwa++ak+ ++w+k  ++++++++ p    ++Wfedg +nv+ nc+drh+++r d+va
  NCBI__GCF_000262405.1:WP_009493644.1  22 GYRAKYEASVKDPEAFWAEEAKR-IDWFKAPTRIKNTNFGPdnvAIRWFEDGVTNVAHNCIDRHLHTRGDQVA 93 
                                           59999*****************5.**************98877789*************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwegd+++e s+k+tY+el++evcr+an++++ Gv kgdrv+iY+pmipea++amlacaR+Ga+hsvvf+Gf
  NCBI__GCF_000262405.1:WP_009493644.1  94 IIWEGDDPSE-SKKITYRELHDEVCRMANIMRNRGVAKGDRVTIYMPMIPEAAYAMLACARLGAIHSVVFGGF 165
                                           ********96.************************************************************** PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220
                                           s+++la+Ri+da++ +++tadeglRgg++++lk +vd+ale++ +  v++vlvv+rtg++v+ ++ grDv+++
  NCBI__GCF_000262405.1:WP_009493644.1 166 SPDSLASRIQDAKSAFIVTADEGLRGGRKVPLKVNVDAALERVGAgVVDHVLVVRRTGSPVN-MVPGRDVYYH 237
                                           *******************************************9999*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e+ e  +s+ec++e++++edplfiLYtsGstG+PkGvlhttgGyl++a++t++yvfd++d+d++wCtaDvGWv
  NCBI__GCF_000262405.1:WP_009493644.1 238 EAAE-LVSDECPCEEMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYASMTHQYVFDYHDGDVYWCTADVGWV 309
                                           ****.5******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYi+ygPLanGattl+fegvptyp+ srfw+vi+k++v+ifYtaPtaiR+lm++gee vkk++++slr+l
  NCBI__GCF_000262405.1:WP_009493644.1 310 TGHSYILYGPLANGATTLMFEGVPTYPTISRFWDVIDKHQVNIFYTAPTAIRSLMQAGEEPVKKTSRKSLRLL 382
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaweWy++vvG+++cpivdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd +gk 
  NCBI__GCF_000262405.1:WP_009493644.1 383 GSVGEPINPEAWEWYHRVVGDGRCPIVDTWWQTETGGILITPLPG-ATKLKPGSATRPFFGVKPQIVDADGKV 454
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           +e  +e g Lvi ++wP+++rt+ygd+erfv+tYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+
  NCBI__GCF_000262405.1:WP_009493644.1 455 LEGATE-GNLVIADSWPGQMRTVYGDHERFVQTYFSTYPGKYFTGDGCRRDQDGYYWITGRVDDVINVSGHRM 526
                                           **8777.79**************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalv+h++v+eaavvg+p++ikg+ i+a+v+l++g+e++ee l+kel ++vrkeigpia+pd i+++
  NCBI__GCF_000262405.1:WP_009493644.1 527 GTAEVESALVAHPKVSEAAVVGYPHDIKGQGIYAYVTLMAGEEPSEE-LRKELVAWVRKEIGPIASPDLIQFA 598
                                           **********************************************5.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           + lPktRsGkimRR+lrkiae+e  +lgd+stl+dp vv++l++
  NCBI__GCF_000262405.1:WP_009493644.1 599 PGLPKTRSGKIMRRILRKIAEDEfGSLGDTSTLADPGVVDDLIT 642
                                           ****************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (652 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: 21.12
//
[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