Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO353_14365 AO353_14365 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_14365
Length = 645
Score = 822 bits (2123), Expect = 0.0
Identities = 399/640 (62%), Positives = 482/640 (75%), Gaps = 5/640 (0%)
Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
S +P V + + Y+ +Y+QS+ PD FW EQAKR LDW P+ +V+ T+
Sbjct: 5 STFPKADAVRQAAQLSQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTG 64
Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
+WFA LNVSYNC+DRHLA+RG+Q AIIWEGDDP+ES +ITY++LH VC+ AN
Sbjct: 65 AA--QWFAGAQLNVSYNCIDRHLAQRGEQTAIIWEGDDPAESLHITYQKLHHCVCRLANV 122
Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
L+ + V +GD V IYMPMIPEA AMLAC RIGA+HSVVFGGFSP++L RI+D + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPDSLRDRILDADCRTV 182
Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
ITADEGVR GK +PLK NVD AL + ++ V+V + T + W + RD+WY ++
Sbjct: 183 ITADEGVRGGKYVPLKQNVDKALLS--CPAVSTVVVVEHTQIEVNWVEGRDLWYHQALRD 240
Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + VFDY+ GEV+WC
Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEVFWC 300
Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP+ +R +VIDKH+V+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFWQVIDKHQVNIFYTAPTALRA 360
Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
+M G ++ + +SLRLLGSVGEPINPEAWDWY+ VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420
Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
SPL A +KPG ATRP FGV P L+D G I GA G L I SWPGQ R++YGD R
Sbjct: 421 SPLVSAQRIKPGCATRPMFGVQPVLLDEHGKEISGAGSGVLAIKSSWPGQIRSVYGDPQR 480
Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
+DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A
Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIA 540
Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
EAAVVG PHD+KGQGIY +VT G E S+AL+ EL V +EIG A PD+IQWAP LP
Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGIEPSDALKKELLAHVSQEIGSFAKPDLIQWAPALP 600
Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
KTRSGKIMRRILRKIA E D LGD STLADP VVA LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVAGLID 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: 1340
Number of extensions: 69
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 AO353_14365 AO353_14365 (acetyl-CoA synthetase)
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.14295.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 1025.2 0.0 0 1025.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 AO353_14365 acetyl-CoA synthetas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 AO353_14365 acetyl-CoA synthetase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1025.0 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99
Alignments for each domain:
== domain 1 score: 1025.0 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrh 66
++++y++ly+++ie+p+ fwa++ak+ l+w +p+++v++++ ++ ++Wf++++lnvsync+drh
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 20 SQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTgAAQWFAGAQLNVSYNCIDRH 84
5789**************************************9999******************* PP
TIGR02188 67 vekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviam 131
+++r +++aiiwegd++ e s ++tY++l++ vcrlanvlk+ Gvkkgdrv+iY+pmipea++am
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 85 LAQRGEQTAIIWEGDDPAE-SLHITYQKLHHCVCRLANVLKSRGVKKGDRVCIYMPMIPEAAYAM 148
*****************96.********************************************* PP
TIGR02188 132 lacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesve 196
lacaRiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rggk ++lk++vd+al +++ +v+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 149 LACARIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKYVPLKQNVDKALLSCP-AVS 212
************************************************************9.7** PP
TIGR02188 197 kvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhtt 261
+v+vv++t+ ev+ w+egrD+w+++++++ +s++c+pe++d+edplfiLYtsGstGkPkGvlhtt
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 213 TVVVVEHTQIEVN-WVEGRDLWYHQALRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTT 275
***********66.**************7.*********************************** PP
TIGR02188 262 gGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfw 326
gGyll+aa+t+kyvfd++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp++srfw
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 276 GGYLLQAAMTFKYVFDYRDGEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFW 340
***************************************************************** PP
TIGR02188 327 eviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcp 391
+vi+k++v+ifYtaPta+Ralm++g e +k ++ slr+lgsvGepinpeaw+Wy++ vG+++cp
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 341 QVIDKHQVNIFYTAPTALRALMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCP 405
***************************************************************** PP
TIGR02188 392 ivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwP 456
ivdtwWqtetGgi+++pl + a +kpg+at+P+fG++++++de+gke++ + gvL+ik++wP
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 406 IVDTWWQTETGGIMLSPLVS-AQRIKPGCATRPMFGVQPVLLDEHGKEISGAGS-GVLAIKSSWP 468
********************.6***************************98777.8********* PP
TIGR02188 457 smlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesal 521
+++r++ygd++r+++tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esal
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 469 GQIRSVYGDPQRMIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESAL 533
***************************************************************** PP
TIGR02188 522 vsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
v h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++ +l+kel ++v++eig++akpd i++++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 534 VLHDSIAEAAVVGYPHDLKGQGIYAFVTPMNGIEPSD-ALKKELLAHVSQEIGSFAKPDLIQWAP 597
*************************************.5************************** PP
TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
+lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 598 ALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVAGLID 640
**************************************98875 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.67
//
[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