Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate Ac3H11_2208 Propionate--CoA ligase (EC 6.2.1.17)
Query= BRENDA::P77495
(628 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_2208
Length = 633
Score = 823 bits (2127), Expect = 0.0
Identities = 388/625 (62%), Positives = 499/625 (79%), Gaps = 2/625 (0%)
Query: 2 SFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRW 61
++++FY++SI+ + FW+EQA+ IDW+TP Q D+SNPPFA+WF G TNLCHNA+DR
Sbjct: 6 TYADFYRQSIDHRDAFWSEQAQLIDWKTPPQQVCDYSNPPFAKWFVGGTTNLCHNAVDRH 65
Query: 62 LEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEA 121
L + AL+A+S+ET+ ER+++F +LH EV +A++L+SLGV++GDRVL+YMPMIAEA
Sbjct: 66 LATRASQAALVAISTETDTERSYSFAELHAEVQRMAAVLQSLGVKKGDRVLIYMPMIAEA 125
Query: 122 HITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDA 181
+LAC RIGA+HSVVFGGFAS S+A+RI+D++PV +VSADAG+RGGK++PYK LLD+A
Sbjct: 126 AFAMLACVRIGALHSVVFGGFASGSLASRIEDSEPVAVVSADAGSRGGKVVPYKPLLDEA 185
Query: 182 ISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYTS 241
I+ ++H+P VL+V+RGLA M GRD +ASLR QH+ VP W++S S LYTS
Sbjct: 186 IALSKHKPAAVLMVNRGLAPMHLQPGRDHAWASLREQHLNTVVPCEWVDSTHPSYTLYTS 245
Query: 242 GTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAGM 301
GTTGKPKGVQRD GGYAVALA SM IF + G V+F SDIGWVVGHSYI+Y PLLAGM
Sbjct: 246 GTTGKPKGVQRDTGGYAVALAASMKHIFDAQPGEVYFATSDIGWVVGHSYIIYGPLLAGM 305
Query: 302 ATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLYL 361
TI+YEGLP PD GVWW+IVEKYQV+ MFSAPTA+RVLKK A + ++++ SL+ L+L
Sbjct: 306 TTIMYEGLPIRPDAGVWWSIVEKYQVTHMFSAPTAVRVLKKQDPAFLTQYNVKSLKALWL 365
Query: 362 AGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYNV 421
AGEP+DEPTA W+ L++P+IDNYWQTE+GWPI+A+A G++ R GSPG +YGY+V
Sbjct: 366 AGEPVDEPTARWIGAALNIPIIDNYWQTETGWPILAVANGIEANAARWGSPGKAVYGYHV 425
Query: 422 QLLNEVTGEP-CGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYW-SLFSRPVYATFDW 479
+LL+E TGE G N+KG++ +EGPLPPGC+QT+W DD RFV TYW S+ R +Y+TFDW
Sbjct: 426 KLLDEATGEELTGANQKGVVAIEGPLPPGCMQTVWRDDARFVNTYWKSIPGRLIYSTFDW 485
Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
GIRDADGYHFILGRTDDVINVAGHRLGTREIEESI+SHP +AEVAVVGV D+LKGQVA+A
Sbjct: 486 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESIASHPNIAEVAVVGVADSLKGQVAMA 545
Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
F + +++ L+ E +M VDSQ+G RP+ V+FVS LPKTRSGK+LRR +Q
Sbjct: 546 FAVARDASGLDSDAARLKLEGEVMKQVDSQLGAVARPSRVYFVSVLPKTRSGKLLRRALQ 605
Query: 600 AICEGRDPGDLTTIDDPASLDQIRQ 624
A+ E RDPGDLTT++DPA+L Q+++
Sbjct: 606 AVAERRDPGDLTTMEDPAALQQVKE 630
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: 1184
Number of extensions: 35
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: 633
Length adjustment: 38
Effective length of query: 590
Effective length of database: 595
Effective search space: 351050
Effective search space used: 351050
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 Ac3H11_2208 (Propionate--CoA ligase (EC 6.2.1.17))
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.aa/TIGR02316.hmm
# target sequence database: /tmp/gapView.3858.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 1095.5 3.6 0 1095.3 3.6 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 Propionate--CoA ligase (EC 6.2.1
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 Propionate--CoA ligase (EC 6.2.1.17)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1095.3 3.6 0 0 2 624 .. 6 630 .. 5 633 .] 0.99
Alignments for each domain:
== domain 1 score: 1095.3 bits; conditional E-value: 0
TIGR02316 2 ayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhle 63
+y ++y++si++ +afw+eqa+ idw+tp+++v d+sn+pfa+wfvgg tnlc+navdrhl+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 6 TYADFYRQSIDHRDAFWSEQAQLIDWKTPPQQVCDYSNPPFAKWFVGGTTNLCHNAVDRHLA 67
699*********************************************************** PP
TIGR02316 64 krgeqlalvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalal 125
+r+ q+alva+s+et++er++++ +lh ev+++a++l++lgv++gdrvliy+pmiaeaa+a+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 68 TRASQAALVAISTETDTERSYSFAELHAEVQRMAAVLQSLGVKKGDRVLIYMPMIAEAAFAM 129
************************************************************** PP
TIGR02316 126 lacarigaihsvvfggfashslaariddatpklivsadagarggkvieykklldaaiaeaqh 187
lac riga+hsvvfggfas sla ri+d++p+ +vsadag+rggkv++yk+lld+aia ++h
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 130 LACVRIGALHSVVFGGFASGSLASRIEDSEPVAVVSADAGSRGGKVVPYKPLLDEAIALSKH 191
************************************************************** PP
TIGR02316 188 kpahvllvdrglaklrrvpgrdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkg 249
kpa vl+v+rgla+++ pgrd +a+lr+qh ++ v++ew++s+ psy lytsgttgkpkg
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 192 KPAAVLMVNRGLAPMHLQPGRDHAWASLREQHLNTVVPCEWVDSTHPSYTLYTSGTTGKPKG 253
************************************************************** PP
TIGR02316 250 vqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeglpt 311
vqrd+ggyavalaasm+ if+a+ g+v+f++sd+gwvvghsyi+y+pllag++t++yeglp+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 254 VQRDTGGYAVALAASMKHIFDAQPGEVYFATSDIGWVVGHSYIIYGPLLAGMTTIMYEGLPI 315
************************************************************** PP
TIGR02316 312 rpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagepldeptarw 373
rpd+gvwwsiveky+v+ mfsapta+rvlkkqd+a l ++++ sl+ l+lagep+deptarw
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 316 RPDAGVWWSIVEKYQVTHMFSAPTAVRVLKKQDPAFLTQYNVKSLKALWLAGEPVDEPTARW 377
************************************************************** PP
TIGR02316 374 isdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvygyrldvldeatgedv.gp 434
i+ al+ p+idnywqtetgwp+la+a+g++ ++++ gspg vygy++++ldeatge+ g+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 378 IGAALNIPIIDNYWQTETGWPILAVANGIEANAARWGSPGKAVYGYHVKLLDEATGEELtGA 439
********************************************************985389 PP
TIGR02316 435 nekgllvvaaplppgclstvwgddarflktyfsafk.rllyssldwgirdedgytfilgrtd 495
n+kg++++++plppgc++tvw ddarf++ty+ ++ rl+ys++dwgird+dgy+filgrtd
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 440 NQKGVVAIEGPLPPGCMQTVWRDDARFVNTYWKSIPgRLIYSTFDWGIRDADGYHFILGRTD 501
**********************************999************************* PP
TIGR02316 496 dvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsvedaddaha 557
dvinvaghrlgtreiees++sh+++aevavvgv+d+lkgqva+afa+ ++a+ ++ +++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 502 DVINVAGHRLGTREIEESIASHPNIAEVAVVGVADSLKGQVAMAFAVARDASGLDSDAARLK 563
************************************************************** PP
TIGR02316 558 lekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaal 619
le+e+m+ v+sqlgavarp+rvy+v+ lpktrsgkllrra+qavae rdpgdltt++dpaal
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 564 LEGEVMKQVDSQLGAVARPSRVYFVSVLPKTRSGKLLRRALQAVAERRDPGDLTTMEDPAAL 625
************************************************************** PP
TIGR02316 620 eqvre 624
+qv+e
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2208 626 QQVKE 630
***97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (628 nodes)
Target sequences: 1 (633 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: 00:00:00.03
# Mc/sec: 10.10
//
[ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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