Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517
Length = 645
Score = 815 bits (2104), Expect = 0.0
Identities = 400/641 (62%), Positives = 481/641 (75%), Gaps = 7/641 (1%)
Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
S +P V + + Y+ +Y+QSV +P FW EQA R LDW P+ TV++ +
Sbjct: 5 STFPKADAVRRAAQLSQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTG 64
Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
+ WFA LNVSYNC+DRHL +RGDQ+AIIWEGDDP++S +ITY++LHE VC+ AN
Sbjct: 65 --EASWFAGAQLNVSYNCIDRHLEKRGDQVAIIWEGDDPADSTSITYKKLHENVCRLANV 122
Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
L+ + V +GD V IYMPMIPEA AMLACTRIGA+HSVVFGGFSP++L RI+D + V
Sbjct: 123 LKNRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182
Query: 184 ITADEGVRAGKKIPLKANVDDALTN-PETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMK 242
ITADEGVR GK + LK NVD AL + P+ SS V+V +RT G + W + RDI Y+ ++
Sbjct: 183 ITADEGVRGGKVVSLKQNVDKALQSCPDVSS---VLVVERTKGLVNWVEGRDIKYQQALR 239
Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYW 302
A C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ EV+W
Sbjct: 240 EASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDDEVFW 299
Query: 303 CTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIR 362
CTADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP +R +VIDKHKV+I YTAPTA+R
Sbjct: 300 CTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDKHKVNIFYTAPTALR 359
Query: 363 AMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVL 422
A+M G ++ +S+RLLG+VGEPINPEAW+WY+ VG+ERCPIVDTWWQTETGG++
Sbjct: 360 ALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVGEERCPIVDTWWQTETGGIM 419
Query: 423 ISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHD 482
+SPL A +KPG AT+P FGV P L+D G I+GA G L I SWP Q R++Y D
Sbjct: 420 LSPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYRDPQ 479
Query: 483 RFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542
R VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +
Sbjct: 480 RMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHENI 539
Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602
AEAA VG PHDIKGQGIYV+VT G ET++ L+ EL V KEIG A PD+IQWAP L
Sbjct: 540 AEAAAVGYPHDIKGQGIYVFVTPMNGVETNDELKKELLALVSKEIGSFAKPDLIQWAPAL 599
Query: 603 PKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
PKTRSGKIMRRILRKIA E D LGD STLADP VV LI+
Sbjct: 600 PKTRSGKIMRRILRKIACNELDNLGDTSTLADPSVVQGLID 640
Lambda K H
0.318 0.135 0.418
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: 1339
Number of extensions: 73
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space: 372091
Effective search space used: 372091
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 PfGW456L13_1517 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.19240.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 1018.1 0.0 0 1017.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1017.9 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.98
Alignments for each domain:
== domain 1 score: 1017.9 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgel 56
++++y++ly++++e+p++fwa++a++ l+w p+e+v++ +l++ ++ Wf++++l
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 20 SQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTgEASWFAGAQL 74
5789*************************************9999********** PP
TIGR02188 57 nvsyncvdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGv 111
nvsync+drh+ekr d+vaiiwegd++ ds ++tY++l+++vcrlanvlk+ Gv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 75 NVSYNCIDRHLEKRGDQVAIIWEGDDPA-DSTSITYKKLHENVCRLANVLKNRGV 128
***************************9.5************************* PP
TIGR02188 112 kkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdaeaklvi 166
kkgdrv+iY+pmipea++amlac+RiGavhsvvf+Gfs+++l++Ri da++++vi
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 129 KKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVI 183
******************************************************* PP
TIGR02188 167 tadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
tadeg+Rggkv++lk++vd+al++++ +v++vlvv+rt+ v+ w+egrD+++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 184 TADEGVRGGKVVSLKQNVDKALQSCP-DVSSVLVVERTKGLVN-WVEGRDIKYQQ 236
*************************9.6**********99955.*********** PP
TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
++++ asa+c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 237 ALRE-ASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVL 290
***6.************************************************** PP
TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviek 331
d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp++srfw+vi+k
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 291 DYRDDEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDK 345
******************************************************* PP
TIGR02188 332 ykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvG 386
+kv+ifYtaPta+Ralm++g e +k++++ s+r+lg+vGepinpeaweWy+++vG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 346 HKVNIFYTAPTALRALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVG 400
******************************************************* PP
TIGR02188 387 kekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeve 441
+e+cpivdtwWqtetGgi+++pl + a +kpg+at+P+fG++++++de+gke++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 401 EERCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKEIK 454
*************************.6***************************9 PP
TIGR02188 442 eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiw 496
+ gvL+ik++wP+++r++y+d++r+v+tYfk ++g+yftGDgarrd+dG++w
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 455 GAGS-GVLAIKSSWPAQIRSVYRDPQRMVDTYFKPYPGYYFTGDGARRDEDGDYW 508
8777.8************************************************* PP
TIGR02188 497 ilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
i+GR+DdvinvsGhr+gtae+esalv he++aeaa+vg+p++ikg+ i++fv+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 509 ITGRIDDVINVSGHRIGTAEVESALVLHENIAEAAAVGYPHDIKGQGIYVFVTPM 563
******************************************************* PP
TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606
+gve+++e l+kel +lv+keig++akpd i+++++lPktRsGkimRR+lrkia
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 564 NGVETNDE-LKKELLALVSKEIGSFAKPDLIQWAPALPKTRSGKIMRRILRKIAC 617
******95.********************************************** PP
TIGR02188 607 ge.ellgdvstledpsvveelke 628
+e ++lgd+stl+dpsvv+ l++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 618 NElDNLGDTSTLADPSVVQGLID 640
******************99875 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (645 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 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.63
//
[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