GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halioglobus japonicus S1-36

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_084200888.1 C0029_RS18225 acetate--CoA ligase

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



>NCBI__GCF_002869505.1:WP_084200888.1
          Length = 643

 Score =  834 bits (2154), Expect = 0.0
 Identities = 412/643 (64%), Positives = 485/643 (75%), Gaps = 6/643 (0%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59
           MS    +PV P    +   D  TYKAMYQ+S+ +PDGF+ + A   L W +P+  V +  
Sbjct: 1   MSEFPTHPV-PANFKDAHIDADTYKAMYQRSIDDPDGFFSQMANDFLSWDQPWDKVME-- 57

Query: 60  FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCK 119
           +D    +  WFA G LNVSYNC+DRHL ER DQ A+IWEGDDPA+S++ITY EL + VCK
Sbjct: 58  YDFIKGEAAWFAGGKLNVSYNCVDRHLPERADQTALIWEGDDPADSKHITYAELKDHVCK 117

Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179
            ANAL+ + V +GD V IYMPMIPEA  AMLACTRIGA+HS+VFGGFSPEAL  RI+D  
Sbjct: 118 LANALKARGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSIVFGGFSPEALKDRILDSD 177

Query: 180 SKVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYED 239
            + VITADEG+R G+K+ LK N D AL      ++   +V +RT G++ WN  RD+WY +
Sbjct: 178 CQTVITADEGVRGGRKVPLKVNADKALE--ACPNVHTCLVVERTSGDVAWNADRDVWYHE 235

Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGE 299
           L+    T C P+ M AE+ LFILYTSGSTGKPKGV HTTGGYLL AA+T + VFDYR GE
Sbjct: 236 LVDGQSTDCEPESMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGE 295

Query: 300 IYWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPT 359
           IYWCTADVGWVTGHTYIVYGPLANGA +L+FEGVP YPD  R  +++DKH+VN  YTAPT
Sbjct: 296 IYWCTADVGWVTGHTYIVYGPLANGAISLMFEGVPTYPDAGRCWEVVDKHQVNTFYTAPT 355

Query: 360 AIRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETG 419
           AIRA+ A G   V  A   SLRLLG+VGEPINPEAWEWY++ VG  RCPI+DTWWQTETG
Sbjct: 356 AIRALQAVGDEPVTRASRVSLRLLGTVGEPINPEAWEWYHRVVGDGRCPIIDTWWQTETG 415

Query: 420 ATLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYG 479
           A +++PLPGA  LKPGSA  PFFGV  AL++  G+ IEG   G LV+  SWP Q RT++G
Sbjct: 416 AHMITPLPGAVPLKPGSATFPFFGVELALLNEDGSEIEGPGAGYLVVKRSWPSQIRTVFG 475

Query: 480 DHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
           DH R +DTYF+ + G YFTGDGA RD DGY+WITGRVDDVLNVSGHRMGTAE+ESA+V H
Sbjct: 476 DHKRLIDTYFRNYPGYYFTGDGATRDEDGYYWITGRVDDVLNVSGHRMGTAEVESALVLH 535

Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWA 599
            ++AEAAVVG PHDIKGQGIY YVT   G EP+E LR EL     KEIGPIA PD+IQWA
Sbjct: 536 EEIAEAAVVGFPHDIKGQGIYAYVTPMQGVEPNEELRQELIALCVKEIGPIAKPDIIQWA 595

Query: 600 PGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLI 642
           PGLPKTRSGKIMRRILRKIA  E D LGD STLADP VV +L+
Sbjct: 596 PGLPKTRSGKIMRRILRKIAENELDSLGDTSTLADPSVVDNLV 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: 1458
Number of extensions: 72
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: 643
Length adjustment: 38
Effective length of query: 613
Effective length of database: 605
Effective search space:   370865
Effective search space used:   370865
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_084200888.1 C0029_RS18225 (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.1678905.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 1027.7   0.0          0 1027.5   0.0    1.0  1  NCBI__GCF_002869505.1:WP_084200888.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002869505.1:WP_084200888.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1027.5   0.0         0         0       3     627 ..      19     638 ..      17     640 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1027.5 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                           ++++yk++y+++i+dp+ f++++a++ l+w++p++kv++ ++ + +++Wf++g+lnvsyncvdrh+ +r+d++
  NCBI__GCF_002869505.1:WP_084200888.1  19 DADTYKAMYQRSIDDPDGFFSQMANDFLSWDQPWDKVMEYDFIKgEAAWFAGGKLNVSYNCVDRHLPERADQT 91 
                                           6799*************************************9999**************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a+iwegd++  ds+++tYael+++vc+lan+lk+ Gvkkgdrv+iY+pmipea++amlac+RiGavhs+vf+G
  NCBI__GCF_002869505.1:WP_084200888.1  92 ALIWEGDDPA-DSKHITYAELKDHVCKLANALKARGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSIVFGG 163
                                           *********9.5************************************************************* PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs+eal++Ri d+++++vitadeg+Rgg++++lk ++d+ale+++ +v+++lvv+rt  +va w+ +rDvw++
  NCBI__GCF_002869505.1:WP_084200888.1 164 FSPEALKDRILDSDCQTVITADEGVRGGRKVPLKVNADKALEACP-NVHTCLVVERTSGDVA-WNADRDVWYH 234
                                           ********************************************9.6*************77.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           elv+ ++s++cepe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyvfd++d++i+wCtaDvGWv
  NCBI__GCF_002869505.1:WP_084200888.1 235 ELVD-GQSTDCEPESMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEIYWCTADVGWV 306
                                           ****.6******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGh+YivygPLanGa +l+fegvptypda+r+wev++k++v++fYtaPtaiRal+++g+e v++ ++ slr+l
  NCBI__GCF_002869505.1:WP_084200888.1 307 TGHTYIVYGPLANGAISLMFEGVPTYPDAGRCWEVVDKHQVNTFYTAPTAIRALQAVGDEPVTRASRVSLRLL 379
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepinpeaweWy++vvG+++cpi+dtwWqtetG+++itplpg a++lkpgsat P+fG+e ++++e+g+e
  NCBI__GCF_002869505.1:WP_084200888.1 380 GTVGEPINPEAWEWYHRVVGDGRCPIIDTWWQTETGAHMITPLPG-AVPLKPGSATFPFFGVELALLNEDGSE 451
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           +e     g+Lv+k++wPs++rt++gd++r+++tYf++++g+yftGDga+rd+dGy+wi+GRvDdv+nvsGhr+
  NCBI__GCF_002869505.1:WP_084200888.1 452 IEGPGA-GYLVVKRSWPSQIRTVFGDHKRLIDTYFRNYPGYYFTGDGATRDEDGYYWITGRVDDVLNVSGHRM 523
                                           *97666.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalv he++aeaavvg+p++ikg+ i+a+v+ ++gve++ee l++el++l  keigpiakpd i+++
  NCBI__GCF_002869505.1:WP_084200888.1 524 GTAEVESALVLHEEIAEAAVVGFPHDIKGQGIYAYVTPMQGVEPNEE-LRQELIALCVKEIGPIAKPDIIQWA 595
                                           **********************************************5.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           + lPktRsGkimRR+lrkiae+e ++lgd+stl+dpsvv++l 
  NCBI__GCF_002869505.1:WP_084200888.1 596 PGLPKTRSGKIMRRILRKIAENElDSLGDTSTLADPSVVDNLV 638
                                           ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (643 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: 23.90
//
[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