Alignments for a candidate for acs in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dinoroseobacter shibae DFL-12

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 3610172 Dshi_3553 acetate--CoA ligase (RefSeq)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Dino:3610172
          Length = 658

 Score =  841 bits (2172), Expect = 0.0
 Identities = 399/630 (63%), Positives = 490/630 (77%), Gaps = 5/630 (0%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLA 78
           I+  +Y  MY  S++ P+ FWGE G+ LDWIKPY KVK+TSFA  +V ++W+EDGTLN+A
Sbjct: 26  IDSSKYSEMYAASVSDPEGFWGEHGRSLDWIKPYTKVKDTSFAHDDVHVRWFEDGTLNVA 85

Query: 79  ANCLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137
           ANC+DRHL   GD+TAII+E DD A  ++HI+Y+ELHR VC+ +N L +LG++KGD V +
Sbjct: 86  ANCIDRHLATRGDQTAIIFEPDDPAEPAQHITYRELHRQVCKLSNVLEDLGVRKGDRVIL 145

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           YMPM+PEAA AMLACARIGA+HS++F GFSP+A++ RI  +++RL+IT+D   R GR  P
Sbjct: 146 YMPMIPEAAYAMLACARIGAIHSIVFAGFSPDALSARINGADARLLITADYAPRGGRQTP 205

Query: 198 LKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAED 257
           LK N D AL +        ++V+KRTGG+  W +GRD  +H+L+ +A +     E+ AE 
Sbjct: 206 LKSNADAALLHTR--DDVKMLVVKRTGGQTTWVDGRDFDYHELMLEADEVQHPVEVEAEH 263

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTG+PKGV+H++GGYL+YAA+T KYVFD H GD+YWCTADVGWVTGHSY++
Sbjct: 264 PLFILYTSGSTGQPKGVVHSSGGYLLYAAMTQKYVFDVHEGDVYWCTADVGWVTGHSYIV 323

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPLA G TT+MFEGVP +P  +R  QV DKH+V   YTAPTAIRALMA+G + +E  D 
Sbjct: 324 YGPLANGGTTVMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTAIRALMAKGPEFVETCDL 383

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
           SSLR+LG+VGEPINPEAW WY   +G  +CP+VDTWWQTETGG ++TPLPGA   K GSA
Sbjct: 384 SSLRVLGTVGEPINPEAWNWYNDLVGKGRCPIVDTWWQTETGGHLLTPLPGAIATKPGSA 443

Query: 438 TRPFFGVQPALVDNEGNP--LEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNM 495
           T PFFGVQP ++D        E   EG L + DSWPGQ RT++GDHERF +TYFS +K  
Sbjct: 444 TLPFFGVQPVVLDPHSGAEITETECEGVLCLKDSWPGQMRTVYGDHERFVKTYFSDYKGY 503

Query: 496 YFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIK 555
           YFSGDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH K+AEAAVVG PH+IK
Sbjct: 504 YFSGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHAKVAEAAVVGYPHDIK 563

Query: 556 GQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRIL 615
           GQ IY YVTL +GEEPS EL  E+R WVR EIGP+A PD++ W   LPKTRSGKIMRRIL
Sbjct: 564 GQGIYCYVTLMNGEEPSEELRKELRTWVRTEIGPIAAPDLIQWAPGLPKTRSGKIMRRIL 623

Query: 616 RKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RKIA  D   LGDTSTLADP VVE L+E +
Sbjct: 624 RKIAEDDFGALGDTSTLADPSVVEDLIENR 653


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: 1413
Number of extensions: 63
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: 652
Length of database: 658
Length adjustment: 38
Effective length of query: 614
Effective length of database: 620
Effective search space:   380680
Effective search space used:   380680
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 3610172 Dshi_3553 (acetate--CoA ligase (RefSeq))
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.28391.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 1010.7   0.0          0 1010.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610172  Dshi_3553 acetate--CoA ligase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610172  Dshi_3553 acetate--CoA ligase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1010.5   0.0         0         0       4     628 ..      28     651 ..      25     652 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1010.5 bits;  conditional E-value: 0
                         TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 
                                        ++y+e+y+ +++dpe fw+++++ +l+w+kp++kv+d+s+++   +v+Wfedg+lnv++nc+drh+++r d++aii
  lcl|FitnessBrowser__Dino:3610172  28 SSKYSEMYAASVSDPEGFWGEHGR-SLDWIKPYTKVKDTSFAHddvHVRWFEDGTLNVAANCIDRHLATRGDQTAII 103
                                       679*********************.6**************99888899***************************** PP

                         TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaeala 154
                                       +e d++ e ++++tY+el+r+vc+l+nvl++lGv+kgdrv++Y+pmipea++amlacaRiGa+hs+vfaGfs++al 
  lcl|FitnessBrowser__Dino:3610172 104 FEPDDPAEPAQHITYRELHRQVCKLSNVLEDLGVRKGDRVILYMPMIPEAAYAMLACARIGAIHSIVFAGFSPDALS 180
                                       ***************************************************************************** PP

                         TIGR02188 155 eRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekeasaec 231
                                        Ri+ a+a+l+itad + Rgg++++lk+++d+al ++ ++v+ +lvvkrtg + ++w++grD+ ++el+ + a++  
  lcl|FitnessBrowser__Dino:3610172 181 ARINGADARLLITADYAPRGGRQTPLKSNADAALLHTRDDVK-MLVVKRTGGQ-TTWVDGRDFDYHELMLE-ADEVQ 254
                                       *************************************99997.899*******.56**************6.99999 PP

                         TIGR02188 232 epekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGa 308
                                       +p ++++e+plfiLYtsGstG+PkGv+h++gGyll+aa+t+kyvfd++++d++wCtaDvGWvtGhsYivygPLanG 
  lcl|FitnessBrowser__Dino:3610172 255 HPVEVEAEHPLFILYTSGSTGQPKGVVHSSGGYLLYAAMTQKYVFDVHEGDVYWCTADVGWVTGHSYIVYGPLANGG 331
                                       999************************************************************************** PP

                         TIGR02188 309 ttllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevv 385
                                       tt++fegvptypdasrfw+v++k+kvt+fYtaPtaiRalm++g e+v+  dlsslrvlg+vGepinpeaw+Wy++ v
  lcl|FitnessBrowser__Dino:3610172 332 TTVMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTAIRALMAKGPEFVETCDLSSLRVLGTVGEPINPEAWNWYNDLV 408
                                       ***************************************************************************** PP

                         TIGR02188 386 GkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eegkeveeeeeggvLvikkpwPsmlrt 461
                                       Gk++cpivdtwWqtetGg+l+tplpg a+++kpgsatlP+fG++++v+d ++g e++e+e +gvL++k++wP+++rt
  lcl|FitnessBrowser__Dino:3610172 409 GKGRCPIVDTWWQTETGGHLLTPLPG-AIATKPGSATLPFFGVQPVVLDpHSGAEITETECEGVLCLKDSWPGQMRT 484
                                       **************************.6*********************999*****99999*************** PP

                         TIGR02188 462 iygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpde 538
                                       +ygd+erfv+tYf+++kg+yf+GDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv+h +vaeaavvg+p++
  lcl|FitnessBrowser__Dino:3610172 485 VYGDHERFVKTYFSDYKGYYFSGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHAKVAEAAVVGYPHD 561
                                       ***************************************************************************** PP

                         TIGR02188 539 ikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdv 614
                                       ikg+ i+++v+l++g+e++ee l+kel+++vr+eigpia+pd i++++ lPktRsGkimRR+lrkiae++  +lgd+
  lcl|FitnessBrowser__Dino:3610172 562 IKGQGIYCYVTLMNGEEPSEE-LRKELRTWVRTEIGPIAAPDLIQWAPGLPKTRSGKIMRRILRKIAEDDfGALGDT 637
                                       ********************5.******************************************************* PP

                         TIGR02188 615 stledpsvveelke 628
                                       stl+dpsvve+l+e
  lcl|FitnessBrowser__Dino:3610172 638 STLADPSVVEDLIE 651
                                       **********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (658 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: 00:00:00.03
# Mc/sec: 12.34
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources