Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695
(651 letters)
>FitnessBrowser__azobra:AZOBR_RS00270
Length = 646
Score = 936 bits (2420), Expect = 0.0
Identities = 443/643 (68%), Positives = 516/643 (80%), Gaps = 3/643 (0%)
Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
MS S +PV+ E+A + DEA Y +Y+QS+ +P+ FW EQ KR+DWIKP++ VK S+
Sbjct: 1 MSDNSFFPVKQEIAKTAYVDEAAYARLYEQSINDPEAFWGEQGKRIDWIKPYSKVKDVSY 60
Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
V IKWF DGTLNVS NC+DRHLA RGDQ AII+EGDDP S++ITY+ELHE+VC+
Sbjct: 61 TGD-VHIKWFYDGTLNVSANCVDRHLATRGDQTAIIFEGDDPGVSKHITYKELHEQVCRL 119
Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
AN L+ V +GD VTIY+PMIPEA AMLAC R+GAIHS+VFGGFSP++L RI+DC S
Sbjct: 120 ANVLKKNGVKKGDRVTIYLPMIPEAAYAMLACARVGAIHSIVFGGFSPDSLKDRIVDCDS 179
Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
VIT+DEG+R G+K+PLKAN D A+ ++ V+V K T GN+ W + RD+WY +
Sbjct: 180 HFVITSDEGLRGGRKVPLKANADKAVA--AAPGVKHVLVVKHTGGNVAWTEGRDLWYHEE 237
Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
+ C P+EM AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDYK GEV
Sbjct: 238 IASVSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYKDGEV 297
Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
YWCTADVGWVTGHSYIVYGPLANGATTL+FEGVP YPDI+R +V+DKHKV+I YTAPTA
Sbjct: 298 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTA 357
Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
IR++M G V+ SSLR+LGSVGEPINPEAW WYY VG RCPIVDTWWQTETGG
Sbjct: 358 IRSLMREGEGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGG 417
Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
+LI+PLPGA KPGSAT+PFFGV P +VDN G +EG EGNL I DSWPGQ RT++GD
Sbjct: 418 ILITPLPGAIGQKPGSATKPFFGVKPVVVDNDGKELEGETEGNLCIADSWPGQMRTVFGD 477
Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
H+RFV TYF TF+G YFTGDG RRD DGYYWITGRVDDV+NVSGHRMGTAE+ESA+VAHP
Sbjct: 478 HERFVQTYFSTFAGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHP 537
Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
KVAEAAVVG PHD+KGQGIY YVTLNAGE +E LR EL WVRKEIGPIASPD+IQW+P
Sbjct: 538 KVAEAAVVGYPHDLKGQGIYAYVTLNAGESPTEELRKELVAWVRKEIGPIASPDLIQWSP 597
Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
GLPKTRSGKIMRRILRKIA E+D LGD STLADP VV LIE
Sbjct: 598 GLPKTRSGKIMRRILRKIAANEHDSLGDTSTLADPTVVTDLIE 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: 1472
Number of extensions: 70
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space: 372704
Effective search space used: 372704
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 AZOBR_RS00270 AZOBR_RS00270 (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.2401618.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 1052.7 0.0 0 1052.5 0.0 1.0 1 FitnessBrowser__azobra:AZOBR_RS00270
Domain annotation for each sequence (and alignments):
>> FitnessBrowser__azobra:AZOBR_RS00270
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1052.5 0.0 0 0 4 628 .. 21 640 .. 18 641 .. 0.98
Alignments for each domain:
== domain 1 score: 1052.5 bits; conditional E-value: 0
TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkv 74
+y++lye++i+dpe+fw++++k +++w+kp++kv+d s + ++kWf dg+lnvs+ncvdrh+++r d++
FitnessBrowser__azobra:AZOBR_RS00270 21 EAAYARLYEQSINDPEAFWGEQGK-RIDWIKPYSKVKDVSYTGdvHIKWFYDGTLNVSANCVDRHLATRGDQT 92
578*********************.5*************9987779*************************** PP
TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
aii+egd++g s+++tY+el+++vcrlanvlk+ Gvkkgdrv+iYlpmipea++amlacaR+Ga+hs+vf+G
FitnessBrowser__azobra:AZOBR_RS00270 93 AIIFEGDDPGV-SKHITYKELHEQVCRLANVLKKNGVKKGDRVTIYLPMIPEAAYAMLACARVGAIHSIVFGG 164
**********7.************************************************************* PP
TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
fs+++l++Rivd+++++vit+deglRgg++++lk+++d+a+++a+ v++vlvvk+tg +va w+egrD+w++
FitnessBrowser__azobra:AZOBR_RS00270 165 FSPDSLKDRIVDCDSHFVITSDEGLRGGRKVPLKANADKAVAAAP-GVKHVLVVKHTGGNVA-WTEGRDLWYH 235
********************************************9.6*************77.********** PP
TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
e++++ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd+kd++++wCtaDvGWv
FitnessBrowser__azobra:AZOBR_RS00270 236 EEIAS-VSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYKDGEVYWCTADVGWV 307
****6.******************************************************************* PP
TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
tGhsYivygPLanGattl+fegvptypd srfw+v++k+kv+ifYtaPtaiR+lm++ge vkk+++sslr+l
FitnessBrowser__azobra:AZOBR_RS00270 308 TGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTAIRSLMREGEGPVKKTSRSSLRIL 380
************************************************************************* PP
TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
gsvGepinpeaw Wyy+vvG+++cpivdtwWqtetGgilitplpg a+ +kpgsat+P+fG++++vvd++gke
FitnessBrowser__azobra:AZOBR_RS00270 381 GSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGGILITPLPG-AIGQKPGSATKPFFGVKPVVVDNDGKE 452
*********************************************.6************************** PP
TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
+e e+e g L+i ++wP+++rt++gd+erfv+tYf+++ g+yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+
FitnessBrowser__azobra:AZOBR_RS00270 453 LEGETE-GNLCIADSWPGQMRTVFGDHERFVQTYFSTFAGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRM 524
**8887.79**************************************************************** PP
TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
gtae+esalv+h++vaeaavvg+p+++kg+ i+a+v+l++g++++ee l+kel ++vrkeigpia+pd i++
FitnessBrowser__azobra:AZOBR_RS00270 525 GTAEVESALVAHPKVAEAAVVGYPHDLKGQGIYAYVTLNAGESPTEE-LRKELVAWVRKEIGPIASPDLIQWS 596
********************************************995.************************* PP
TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
+ lPktRsGkimRR+lrkia++e ++lgd+stl+dp+vv +l+e
FitnessBrowser__azobra:AZOBR_RS00270 597 PGLPKTRSGKIMRRILRKIAANEhDSLGDTSTLADPTVVTDLIE 640
***********************99**************99986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (646 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 31.93
//
[ok]
This GapMind analysis is from Apr 09 2024. 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