GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pedobacter sp. GW460-11-11-14-LB5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate CA265_RS16340 CA265_RS16340 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS16340 CA265_RS16340
           acetate--CoA ligase
          Length = 631

 Score =  733 bits (1891), Expect = 0.0
 Identities = 360/625 (57%), Positives = 455/625 (72%), Gaps = 10/625 (1%)

Query: 22  QQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANC 81
           +QYE  Y++S+  P+ FWGE  +   W KP+ KV + +F   N  IKW+E   LN+  NC
Sbjct: 7   KQYEEDYKKSVENPEQFWGEVAQNFQWRKPWFKVLSWNFNEPN--IKWFEGAKLNITENC 64

Query: 82  LDRHLQENGDRTAIIWEGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMP 140
           LDRHL  NGD+ AI+WE ++  + S   +YK LH  VCRFAN L   G KKGD + IYMP
Sbjct: 65  LDRHLATNGDKPAIVWEPNNPEEESVTYTYKMLHERVCRFANVLKRNGAKKGDRICIYMP 124

Query: 141 MVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKK 200
           MVPE A+A+LACARIGAVHSVIFGGFS +++A RI DS  ++VIT+D   R  + IPLK 
Sbjct: 125 MVPELAIAVLACARIGAVHSVIFGGFSAKSIADRINDSKCKVVITADGSYRGNKQIPLKD 184

Query: 201 NVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLF 260
            +DDAL      +VE  +VL      +   +GRD+WW D V+  +D  +AEEM+AED LF
Sbjct: 185 VIDDALIG--CPTVEKCIVLTHIRTPVSMLKGRDVWWEDEVKHVNDICEAEEMDAEDMLF 242

Query: 261 ILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGP 320
           ILYTSGSTGKPKGV+HT GGY+VYA  TF  VF+Y PG++Y+CTAD+GW+TGHSY++YGP
Sbjct: 243 ILYTSGSTGKPKGVVHTCGGYMVYAGYTFSNVFNYQPGEVYFCTADIGWITGHSYIVYGP 302

Query: 321 LACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSL 380
           L+ GAT+++FEG+P +PTP+R   +V+KH+VN LYTAPTAIR+LM+ GD  + G D SS+
Sbjct: 303 LSQGATSVLFEGIPTYPTPSRFWDIVEKHKVNTLYTAPTAIRSLMSYGDDPLNGKDLSSI 362

Query: 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRP 440
           R+LGSVGEPIN EAW W+ +KIG+ K P+VDTWWQTETGG MI+P+   T  K   AT P
Sbjct: 363 RVLGSVGEPINEEAWHWFDEKIGHGKAPIVDTWWQTETGGIMISPIATVTPTKPSFATLP 422

Query: 441 FFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSG 499
             G+QP LVD  GN +EG    G+L I   WPG  RT +GDHER +QTYFST+ N+YF+G
Sbjct: 423 LPGIQPILVDENGNEIEGNGVMGNLCIKFPWPGMLRTTYGDHERCKQTYFSTYDNLYFTG 482

Query: 500 DGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAI 559
           DG  RDEDGYY ITGRVDDVLNVSGHR+GTAE+E+A+  H  + E+AVVG PH++KGQ I
Sbjct: 483 DGCLRDEDGYYRITGRVDDVLNVSGHRIGTAEVENAINMHAGVVESAVVGYPHDVKGQGI 542

Query: 560 YAYVTL--NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617
           YA+V     HGE    +   ++   V + IG +A PD + +   LPKTRSGKIMRRILRK
Sbjct: 543 YAFVIYPEMHGEAELSK--KDILQTVTRVIGAIAKPDKILFVSGLPKTRSGKIMRRILRK 600

Query: 618 IAAGDTSNLGDTSTLADPGVVEKLL 642
           IA GDTSNLGDTSTL DPGVVE+++
Sbjct: 601 IAEGDTSNLGDTSTLLDPGVVEEII 625


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: 1327
Number of extensions: 59
Number of successful extensions: 6
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: 631
Length adjustment: 38
Effective length of query: 614
Effective length of database: 593
Effective search space:   364102
Effective search space used:   364102
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 CA265_RS16340 CA265_RS16340 (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.9242.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.2e-291  953.5   0.0   2.6e-291  953.3   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS16340  CA265_RS16340 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS16340  CA265_RS16340 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  953.3   0.0  2.6e-291  2.6e-291       2     628 ..       4     626 ..       3     627 .. 0.98

  Alignments for each domain:
  == domain 1  score: 953.3 bits;  conditional E-value: 2.6e-291
                                  TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhve 68 
                                                ++ ++y+e y++++e+pe+fw++ a+ +++w kp+ kvl++++++ ++kWfe+++ln++ nc+drh++
  lcl|FitnessBrowser__Pedo557:CA265_RS16340   4 TSFKQYEEDYKKSVENPEQFWGEVAQ-NFQWRKPWFKVLSWNFNEpNIKWFEGAKLNITENCLDRHLA 70 
                                                5789*********************9.5**************9888********************** PP

                                  TIGR02188  69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaR 136
                                                ++ dk ai+we ++++e+s ++tY+ l+++vcr+anvlk+ G kkgdr++iY+pm+pe++ia+lacaR
  lcl|FitnessBrowser__Pedo557:CA265_RS16340  71 TNGDKPAIVWEPNNPEEESVTYTYKMLHERVCRFANVLKRNGAKKGDRICIYMPMVPELAIAVLACAR 138
                                                ******************************************************************** PP

                                  TIGR02188 137 iGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrt 204
                                                iGavhsv+f+Gfsa+++a+Ri+d+++k+vitad+++Rg+k+i+lk+++d+al  ++ +vek++v+ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 139 IGAVHSVIFGGFSAKSIADRINDSKCKVVITADGSYRGNKQIPLKDVIDDALIGCP-TVEKCIVLTHI 205
                                                *******************************************************9.7********** PP

                                  TIGR02188 205 geevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltv 272
                                                 ++v+ + +grDvwwe++v++ +++ ce+e++d+ed+lfiLYtsGstGkPkGv+ht gGy+++a +t+
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 206 RTPVS-MLKGRDVWWEDEVKH-VNDICEAEEMDAEDMLFILYTSGSTGKPKGVVHTCGGYMVYAGYTF 271
                                                ***76.**************6.********************************************** PP

                                  TIGR02188 273 kyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYta 340
                                                  vf+++++++++CtaD+GW+tGhsYivygPL++Gat++lfeg+ptyp++srfw+++ek+kv+++Yta
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 272 SNVFNYQPGEVYFCTADIGWITGHSYIVYGPLSQGATSVLFEGIPTYPTPSRFWDIVEKHKVNTLYTA 339
                                                ******************************************************************** PP

                                  TIGR02188 341 PtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitp 408
                                                PtaiR+lm +g++ ++ +dlss+rvlgsvGepin eaw+W+ e++G++k+pivdtwWqtetGgi+i+p
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 340 PTAIRSLMSYGDDPLNGKDLSSIRVLGSVGEPINEEAWHWFDEKIGHGKAPIVDTWWQTETGGIMISP 407
                                                ******************************************************************** PP

                                  TIGR02188 409 lpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkk 476
                                                +++ +t++kp+ atlPl+Gi++ +vde+g+e+e +   g L+ik pwP+mlrt ygd+er  +tYf++
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 408 IAT-VTPTKPSFATLPLPGIQPILVDENGNEIEGNGVMGNLCIKFPWPGMLRTTYGDHERCKQTYFST 474
                                                ***.6****************************666669***************************** PP

                                  TIGR02188 477 lkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeai 544
                                                +++lyftGDg+ rd+dGy+ i+GRvDdv+nvsGhr+gtae+e+a+  h  v e+avvg+p+++kg+ i
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 475 YDNLYFTGDGCLRDEDGYYRITGRVDDVLNVSGHRIGTAEVENAINMHAGVVESAVVGYPHDVKGQGI 542
                                                ******************************************************************** PP

                                  TIGR02188 545 vafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ell 611
                                                +afv+  e + e e   +k++ ++v++ ig+iakpdkil+v+ lPktRsGkimRR+lrkiaeg+ ++l
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 543 YAFVIYPEMHGEAE-LSKKDILQTVTRVIGAIAKPDKILFVSGLPKTRSGKIMRRILRKIAEGDtSNL 609
                                                *****999888777.5899*********************************************99** PP

                                  TIGR02188 612 gdvstledpsvveelke 628
                                                gd+stl dp vvee+++
  lcl|FitnessBrowser__Pedo557:CA265_RS16340 610 GDTSTLLDPGVVEEIIA 626
                                                **************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (631 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.28
//
[ok]

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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