Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate N515DRAFT_0016 N515DRAFT_0016 propionyl-CoA synthetase
Query= BRENDA::P77495
(628 letters)
>FitnessBrowser__Dyella79:N515DRAFT_0016
Length = 630
Score = 771 bits (1992), Expect = 0.0
Identities = 370/628 (58%), Positives = 475/628 (75%), Gaps = 5/628 (0%)
Query: 1 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
M + FY+ SI PE FWAEQA+ IDWQTP Q LD+S PPF RWF G TNLC+NAIDR
Sbjct: 1 MDYETFYRHSIEAPEAFWAEQAQLIDWQTPPRQVLDYSRPPFRRWFVGGTTNLCYNAIDR 60
Query: 61 WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
LE + + LAL+A+S+ET R ++RQLH EVN A++L +L VQRGDRV++Y+P IAE
Sbjct: 61 HLEARGDQLALVAISTETGLTRELSYRQLHREVNVFAAVLAALDVQRGDRVVIYLPNIAE 120
Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
A +LACAR+GAIHSVVFGGFA+H++A RIDDA+P L+++ADAG RGGK+IPYK L+D
Sbjct: 121 AVFAMLACARLGAIHSVVFGGFAAHNLALRIDDAQPKLLIAADAGMRGGKVIPYKPLVDA 180
Query: 181 AISQAQHQPRHVLLVDRGL-AKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILY 239
A+ Q+ P HVL+VDRGL +M RV+GRD+D+A LR H A VPVAWLESNE S +LY
Sbjct: 181 ALEQSAAPPPHVLIVDRGLDPQMTRVAGRDLDYAQLRKAHEQAEVPVAWLESNEPSYLLY 240
Query: 240 TSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLA 299
TSGTTGKPKG+QRDVGGYAVA+A S+ IF G V F SD+GW VGHSY VY PL+A
Sbjct: 241 TSGTTGKPKGIQRDVGGYAVAMAMSVRYIFDIAPGQVMFSTSDVGWAVGHSYNVYGPLIA 300
Query: 300 GMATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVL 359
G +++YEGLPT PD G+WW + E+Y V MFS+PT IRVLKK A +RK+DLSSL+ L
Sbjct: 301 GATSLLYEGLPTRPDPGIWWYLCERYSVRTMFSSPTGIRVLKKQDPAWLRKYDLSSLQWL 360
Query: 360 YLAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGY 419
+LAGEPLDEPTA W+++ L VPVIDNYWQTE+GWP + + GL+ + + GSPG+P GY
Sbjct: 361 FLAGEPLDEPTAHWITDGLGVPVIDNYWQTETGWPAITLMPGLELKRVKFGSPGLPAPGY 420
Query: 420 NVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDW 479
+++++E TGE KG+LV E PLPPGC+ T+WGDD R++ +Y+ F +Y++ DW
Sbjct: 421 RMKVIDEATGEEAAPGHKGVLVFEPPLPPGCLSTVWGDDERYLSSYFGHFKELLYSSLDW 480
Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
IRD GY ILGRTDDVINVAGHRLGTREIEES+++HP VAE AV+GV+D LKGQV V
Sbjct: 481 AIRDEHGYTTILGRTDDVINVAGHRLGTREIEESVATHPAVAEAAVIGVRDELKGQVPVV 540
Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
F K+ + VA + ++ ++ Q+G RP+ V+ V+ LPKTRSGK+LRR++Q
Sbjct: 541 FATLKQDAGTQAGQVAQAMQQRVV----DQLGGIARPSRVYVVNALPKTRSGKLLRRSLQ 596
Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAME 627
A+ E RDPGDL+T+DDP +L++IR+A+E
Sbjct: 597 ALAEQRDPGDLSTLDDPGALEEIRRALE 624
Lambda K H
0.320 0.136 0.422
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: 1237
Number of extensions: 45
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: 628
Length of database: 630
Length adjustment: 38
Effective length of query: 590
Effective length of database: 592
Effective search space: 349280
Effective search space used: 349280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)
Align candidate N515DRAFT_0016 N515DRAFT_0016 (propionyl-CoA synthetase)
to HMM TIGR02316 (prpE: propionate--CoA ligase (EC 6.2.1.17))
# 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/TIGR02316.hmm
# target sequence database: /tmp/gapView.18834.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02316 [M=628]
Accession: TIGR02316
Description: propion_prpE: propionate--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 1154.0 0.0 0 1153.8 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 N515DRAFT_0016 propionyl-CoA syn
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 N515DRAFT_0016 propionyl-CoA synthetase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1153.8 0.0 0 0 1 628 [] 1 625 [. 1 625 [. 0.99
Alignments for each domain:
== domain 1 score: 1153.8 bits; conditional E-value: 0
TIGR02316 1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrg 66
m ye +y+ sie peafwaeqa+ idwqtp+ +vld+s++pf+rwfvgg tnlcyna+drhle rg
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 1 MDYETFYRHSIEAPEAFWAEQAQLIDWQTPPRQVLDYSRPPFRRWFVGGTTNLCYNAIDRHLEARG 66
68**************************************************************** PP
TIGR02316 67 eqlalvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarig 132
+qlalva+s+etg +r+l+yrqlhrevn++a++l al v+rgdrv+iylp+iaea++a+lacar+g
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 67 DQLALVAISTETGLTRELSYRQLHREVNVFAAVLAALDVQRGDRVVIYLPNIAEAVFAMLACARLG 132
****************************************************************** PP
TIGR02316 133 aihsvvfggfashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrg 198
aihsvvfggfa+h+la+ridda+pkl+++adag+rggkvi+yk+l+daa++++ +p+hvl+vdrg
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 133 AIHSVVFGGFAAHNLALRIDDAQPKLLIAADAGMRGGKVIPYKPLVDAALEQSAAPPPHVLIVDRG 198
****************************************************************** PP
TIGR02316 199 lak.lrrvpgrdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaa 263
l++ ++rv+grd+dya lr+ he+a+v+v+wlesnepsy+lytsgttgkpkg+qrdvggyava+a+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 199 LDPqMTRVAGRDLDYAQLRKAHEQAEVPVAWLESNEPSYLLYTSGTTGKPKGIQRDVGGYAVAMAM 264
**99************************************************************** PP
TIGR02316 264 smdaifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsv 329
s+ if++ g+v+fs+sdvgw+vghsy+vy+pl+ag++++lyeglptrpd+g+ww ++e+y v++
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 265 SVRYIFDIAPGQVMFSTSDVGWAVGHSYNVYGPLIAGATSLLYEGLPTRPDPGIWWYLCERYSVRT 330
****************************************************************** PP
TIGR02316 330 mfsaptairvlkkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpv 395
mfs+pt+irvlkkqd+a+lrk+dlssl++lflagepldepta+wi+d+lg+pvidnywqtetgwp
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 331 MFSSPTGIRVLKKQDPAWLRKYDLSSLQWLFLAGEPLDEPTAHWITDGLGVPVIDNYWQTETGWPA 396
****************************************************************** PP
TIGR02316 396 laiarglddkpvklgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarf 461
+++++gl+ k vk+gspglp +gyr++v+deatge+++p+ kg+lv ++plppgclstvwgdd r+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 397 ITLMPGLELKRVKFGSPGLPAPGYRMKVIDEATGEEAAPGHKGVLVFEPPLPPGCLSTVWGDDERY 462
****************************************************************** PP
TIGR02316 462 lktyfsafkrllyssldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvg 527
l +yf++fk+llyssldw+irde gyt+ilgrtddvinvaghrlgtreieesv++h+avae+av+g
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 463 LSSYFGHFKELLYSSLDWAIRDEHGYTTILGRTDDVINVAGHRLGTREIEESVATHPAVAEAAVIG 528
****************************************************************** PP
TIGR02316 528 vkdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarparvyvvaalpktrsgkl 593
v+delkgqv+v+fa+lk+ + + +a +++++++ v+ qlg +arp+rvyvv+alpktrsgkl
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 529 VRDELKGQVPVVFATLKQDA--GT--QAGQVAQAMQQRVVDQLGGIARPSRVYVVNALPKTRSGKL 590
*****************433..33..34456678999***************************** PP
TIGR02316 594 lrraiqavaegrdpgdlttiddpaaleqvrealee 628
lrr++qa+ae rdpgdl+t+ddp+ale++r+ale+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 591 LRRSLQALAEQRDPGDLSTLDDPGALEEIRRALER 625
*********************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (628 nodes)
Target sequences: 1 (630 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: 7.78
//
[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 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