Alignments for a candidate for acs in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Marinomonas arctica 328

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_111606505.1 DK187_RS06350 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_003259225.1:WP_111606505.1
          Length = 652

 Score =  822 bits (2122), Expect = 0.0
 Identities = 405/632 (64%), Positives = 480/632 (75%), Gaps = 5/632 (0%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLA 78
           ++  ++E  YQ+SI  PD FWG +GK LDW  PY KVKNTSF  G VSIKW+EDG LN+A
Sbjct: 18  VSQAEFEKRYQESIENPDQFWGREGKRLDWFAPYSKVKNTSFKRGQVSIKWFEDGELNVA 77

Query: 79  ANCLDRHLQENGDRTAIIWEGDDASQSK-HISYKELHRDVCRFANTLLELGIKKGDVVAI 137
            NC+DRHL  + ++ A   EGD  S  K  I+Y+ LH +V R AN L   G+KKGD VAI
Sbjct: 78  YNCIDRHLALSANKVAYYCEGDKESDDKIAITYQTLHDEVGRLANLLKRQGVKKGDRVAI 137

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           YMPM+P+A  AMLACARIGA+HSVIFGGFS  A+A R+ D    LVIT+DEG RAG +IP
Sbjct: 138 YMPMIPQAVYAMLACARIGAIHSVIFGGFSAHAIADRLNDCEVTLVITADEGRRAGNTIP 197

Query: 198 LKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAED 257
           LK NVD AL N    SVE VVV + T   + W EGRDL W   V+  S Q  AE MNAED
Sbjct: 198 LKHNVDMALSNNACPSVEAVVVYRYTQKDVPWFEGRDLDWAAEVKNESTQCPAEPMNAED 257

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTGKPKGV+HTTGGYLVYA+LT + VFD  P DIYWC ADVGW+TGHSY++
Sbjct: 258 PLFILYTSGSTGKPKGVVHTTGGYLVYASLTHELVFDLKPDDIYWCAADVGWITGHSYMV 317

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPLA GAT+++FEGVP +P   R+ +VVDK  V ILYTAPTAIRALMA+GD+A   + R
Sbjct: 318 YGPLANGATSILFEGVPTYPDSGRIGRVVDKFGVTILYTAPTAIRALMAKGDEATRSSHR 377

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
            SLR+LGSVGEPINPEAW WY+ +IG   CP+VDTWWQTETGG M++P     ++K GS 
Sbjct: 378 DSLRVLGSVGEPINPEAWSWYYSEIGKSSCPIVDTWWQTETGGMMMSPRIVQADVKPGSC 437

Query: 438 TRPFFGVQPALVDNEG---NPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKN 494
           T P +GV PALVD +G   N      +G LVITDSWPGQART++GDH+RFEQTYFSTF+ 
Sbjct: 438 TGPLYGVLPALVDAQGIVLNEQGVQVDGGLVITDSWPGQARTVYGDHDRFEQTYFSTFEG 497

Query: 495 MYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNI 554
           MYF+GDGA RD DG+YWITGR+DDVLNVSGHRLGTAEIESALVAHP +AEAA+VG PH+I
Sbjct: 498 MYFTGDGASRDADGHYWITGRMDDVLNVSGHRLGTAEIESALVAHPAVAEAAIVGYPHDI 557

Query: 555 KGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHW-TDSLPKTRSGKIMRR 613
           KGQ IY YV+   G  P  EL   ++ +VR+EIGP+ATPD++ W +  LPKTRSGKIMRR
Sbjct: 558 KGQGIYVYVSAVAGVVPDEELTKSLKQFVRQEIGPIATPDLIQWASKGLPKTRSGKIMRR 617

Query: 614 ILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           ILRKIAA +   LGDTSTLADP VV+ L+E +
Sbjct: 618 ILRKIAANEHDQLGDTSTLADPSVVDDLIENR 649


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: 1391
Number of extensions: 47
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: 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_111606505.1 DK187_RS06350 (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.1241784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-294  963.6   0.0   2.3e-294  963.4   0.0    1.0  1  NCBI__GCF_003259225.1:WP_111606505.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003259225.1:WP_111606505.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  963.4   0.0  2.3e-294  2.3e-294       4     628 ..      20     647 ..      17     648 .. 0.97

  Alignments for each domain:
  == domain 1  score: 963.4 bits;  conditional E-value: 2.3e-294
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           + e+++ y+e+ie+p++fw++++k +l+w+ p++kv+++s++    ++kWfedgelnv+ync+drh++ +++k
  NCBI__GCF_003259225.1:WP_111606505.1  20 QAEFEKRYQESIENPDQFWGREGK-RLDWFAPYSKVKNTSFKRgqvSIKWFEDGELNVAYNCIDRHLALSANK 91 
                                           568999******************.5***************988889************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           va   egd+e++d+ ++tY+ l++ev rlan+lk++GvkkgdrvaiY+pmip+av+amlacaRiGa+hsv+f+
  NCBI__GCF_003259225.1:WP_111606505.1  92 VAYYCEGDKESDDKIAITYQTLHDEVGRLANLLKRQGVKKGDRVAIYMPMIPQAVYAMLACARIGAIHSVIFG 164
                                           ********99999************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfsa+a+a+R++d+e  lvitadeg R g++i+lk++vd al++  + sve v+v++ t+++v  w egrD+ 
  NCBI__GCF_003259225.1:WP_111606505.1 165 GFSAHAIADRLNDCEVTLVITADEGRRAGNTIPLKHNVDMALSNNACpSVEAVVVYRYTQKDVP-WFEGRDLD 236
                                           *******************************************99999**************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           w  +v+ ++s++c++e++++edplfiLYtsGstGkPkGv+httgGyl++a+lt+++vfd+k++di+wC+aDvG
  NCBI__GCF_003259225.1:WP_111606505.1 237 WAAEVK-NESTQCPAEPMNAEDPLFILYTSGSTGKPKGVVHTTGGYLVYASLTHELVFDLKPDDIYWCAADVG 308
                                           ******.5***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           W+tGhsY+vygPLanGat++lfegvptypd++r+ +v++k++vti+YtaPtaiRalm++g+e++++ +++slr
  NCBI__GCF_003259225.1:WP_111606505.1 309 WITGHSYMVYGPLANGATSILFEGVPTYPDSGRIGRVVDKFGVTILYTAPTAIRALMAKGDEATRSSHRDSLR 381
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           vlgsvGepinpeaw+Wyy+++Gk++cpivdtwWqtetGg++++p     +++kpgs+t Pl+G+ +++vd +g
  NCBI__GCF_003259225.1:WP_111606505.1 382 VLGSVGEPINPEAWSWYYSEIGKSSCPIVDTWWQTETGGMMMSPRIV-QADVKPGSCTGPLYGVLPALVDAQG 453
                                           ********************************************999.59*********************** PP

                             TIGR02188 438 keve.ee.eeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                             ++ ++ + +g Lvi+++wP+++rt+ygd++rf +tYf++++g+yftGDga rd+dG++wi+GR+Ddv+nvs
  NCBI__GCF_003259225.1:WP_111606505.1 454 IVLNeQGvQVDGGLVITDSWPGQARTVYGDHDRFEQTYFSTFEGMYFTGDGASRDADGHYWITGRMDDVLNVS 526
                                           9999533144599************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghrlgtaeiesalv+h+avaeaa+vg+p++ikg+ i+++v   +gv +dee l+k+lk+ vr+eigpia+pd 
  NCBI__GCF_003259225.1:WP_111606505.1 527 GHRLGTAEIESALVAHPAVAEAAIVGYPHDIKGQGIYVYVSAVAGVVPDEE-LTKSLKQFVRQEIGPIATPDL 598
                                           *************************************************95.********************* PP

                             TIGR02188 582 ilvve.elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i++++  lPktRsGkimRR+lrkia++e ++lgd+stl+dpsvv++l+e
  NCBI__GCF_003259225.1:WP_111606505.1 599 IQWASkGLPKTRSGKIMRRILRKIAANEhDQLGDTSTLADPSVVDDLIE 647
                                           ***8626*********************9****************9987 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: 21.51
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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