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)
>FitnessBrowser__Pedo557:CA265_RS16340
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.32661.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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.80
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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