Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate Synpcc7942_1037 Synpcc7942_1037 arginine decarboxylase
Query= BRENDA::P74576
(695 letters)
>FitnessBrowser__SynE:Synpcc7942_1037
Length = 647
Score = 843 bits (2178), Expect = 0.0
Identities = 420/661 (63%), Positives = 514/661 (77%), Gaps = 20/661 (3%)
Query: 28 AGVKTDSNPQAIA-QDRRWTIDDSENLYRITGWGEPYFSINAAGHVTVSPQADHGGALDL 86
A +T P A+A + ++W I+DSE LYRI GWGEPYF INAAGH+TVSPQ D GG+LDL
Sbjct: 2 AAEQTAIAPLAVAVESQQWRIEDSEALYRIQGWGEPYFGINAAGHITVSPQGDRGGSLDL 61
Query: 87 YELVKGLRQRNIGLPLLLRFSDILADRINRLNAAFARGIARYRYPNTYRGVYPIKCNQHR 146
YELV+ LR+R + LPLL+RF DIL DRI RLNA FA+ IARY Y YRGV+P+KCNQ R
Sbjct: 62 YELVEALRRRGLNLPLLIRFPDILEDRIERLNACFAKAIARYNYAGEYRGVFPVKCNQQR 121
Query: 147 HIVESLVRYGTPYNFGLEAGSKPELMIALAMLQPQENPEPDQQNQPLLICNGYKDREYIE 206
H++ESLV YG P+ FGLEAGSKPEL+IALA L LLICNGYKDR+YIE
Sbjct: 122 HLIESLVNYGRPFQFGLEAGSKPELLIALAHLDTPG---------ALLICNGYKDRDYIE 172
Query: 207 TALLARRLGHRPIIVVEQVAEVALAIEISSNLGIKPILGVRAKLSTQGMGRWGISTGDRA 266
TA+L RRLG PI+V+EQ+ EV +AI S LGI+PILGVRAKL+ +GMGRWG S GDRA
Sbjct: 173 TAILGRRLGKTPILVIEQLEEVDVAIAASQRLGIEPILGVRAKLNARGMGRWGSSAGDRA 232
Query: 267 KFGLTIPEMLTAIEQLRRADMLDSLQLLHFHIGSQISSISVIKEAMTEASQIFVQLAKLG 326
KFGLT+PE++ A+E+L+ A++L LQLLHFHIGSQIS ISV+K+A+ EA+QI+VQLA LG
Sbjct: 233 KFGLTMPEIVAAVEKLQAANLLHCLQLLHFHIGSQISDISVLKDAIQEAAQIYVQLAALG 292
Query: 327 ANMRYLDVGGGLGVDYDGSKTNFYASKNYNIQNYVNDVISAVQDACVAAEVPCPVLISES 386
A+MRYLDVGGGLGVDYDGSKTNF+ASKNYN+Q Y NDV++ ++DAC A + P L SES
Sbjct: 293 ADMRYLDVGGGLGVDYDGSKTNFHASKNYNMQTYANDVVATIKDACQAHRLAVPTLTSES 352
Query: 387 GRAIASHQSVLIFDVVATNDI-NPPLPKVKGKDHAILRNLMETWETITVDNYQEAYHDVE 445
GRAIASHQSVL+FDV+ ++++ + + +D AI+R L E E I ++N QE YHD
Sbjct: 353 GRAIASHQSVLVFDVLGSSEVPRAAVEPPQEEDSAIVRTLYEVLEAIALENLQECYHDAF 412
Query: 446 QFKTEAISLFNFGYLGLKERAKAEELYWACCRKILQICRQQEYVPDDLENLEVNLASIYY 505
+ K +A+S F GYL L ERAKAE L+W+CC +I + +Q + +P+DLE+LE +ASIYY
Sbjct: 413 KLKEDAVSAFRLGYLSLTERAKAERLFWSCCHRIQEFLKQLDRIPEDLEDLERVMASIYY 472
Query: 506 ANMSVFQSAPDSWAIDQLFPIMPIHRLDEEPTQRGILADITCDSDGKIDQFIDLRDVKSV 565
N+SVFQSAPD+WAIDQLFPIMPIHRL+EEP QR LAD+TCDSDGKID+FIDL DVKS
Sbjct: 473 VNLSVFQSAPDTWAIDQLFPIMPIHRLNEEPNQRVTLADLTCDSDGKIDRFIDLLDVKST 532
Query: 566 LELHPLIEVHQPGTPPRVEPYYLGMFLVGAYQEIMGNLHNLFGDINVVHIQMNPKGYQIE 625
LELH L QP +PY LGMFL GAYQEIMGNLHNLFGD N VHI++ PKGY IE
Sbjct: 533 LELHSL----QPD-----QPYVLGMFLGGAYQEIMGNLHNLFGDTNAVHIKLTPKGYSIE 583
Query: 626 HLVRGDTIAEVLGYVQYDPEDLLENMRRYCEQAMEDKRMSLEEAQLLLENYERSLLQYTY 685
H+V+GDT+ EVLGYVQYD E LLE +R+ E A++ ++SL+EAQ LL +YE L +YTY
Sbjct: 584 HVVKGDTMGEVLGYVQYDTEQLLERLRQQTEAALQQDQISLDEAQRLLRHYEEGLQRYTY 643
Query: 686 L 686
L
Sbjct: 644 L 644
Lambda K H
0.319 0.137 0.402
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: 1142
Number of extensions: 41
Number of successful extensions: 4
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: 695
Length of database: 647
Length adjustment: 39
Effective length of query: 656
Effective length of database: 608
Effective search space: 398848
Effective search space used: 398848
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 Synpcc7942_1037 Synpcc7942_1037 (arginine decarboxylase)
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))
# 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/TIGR01273.hmm
# target sequence database: /tmp/gapView.1790.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01273 [M=624]
Accession: TIGR01273
Description: speA: arginine decarboxylase
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1e-238 779.8 0.0 1.1e-238 779.6 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1037 Synpcc7942_1037 arginine decarbo
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1037 Synpcc7942_1037 arginine decarboxylase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 779.6 0.0 1.1e-238 1.1e-238 1 624 [] 20 645 .. 20 645 .. 0.98
Alignments for each domain:
== domain 1 score: 779.6 bits; conditional E-value: 1.1e-238
TIGR01273 1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqk 69
w++e+s+++Y+i+gWg++yf +n++G+++v+p+g++ + dl+elv++++ +gl+lPll+rFpdil++
lcl|FitnessBrowser__SynE:Synpcc7942_1037 20 WRIEDSEALYRIQGWGEPYFGINAAGHITVSPQGDR-GGSLDLYELVEALRRRGLNLPLLIRFPDILED 87
78999****************************998.99****************************** PP
TIGR01273 70 rikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekp 137
ri++lna F++ai +++Ya++y++v+P+K+nqqr+++e+lv+ g ++GLEaGsKpElliala++++p
lcl|FitnessBrowser__SynE:Synpcc7942_1037 88 RIERLNACFAKAIARYNYAGEYRGVFPVKCNQQRHLIESLVNYGrPFQFGLEAGSKPELLIALAHLDTP 156
********************************************99*********************** PP
TIGR01273 138 kavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwa 206
+a+++cnGyKDr+yie+a+++r+lg ++vie+leE+d+ i+ +++lg++P lG+R++L+++g g+w+
lcl|FitnessBrowser__SynE:Synpcc7942_1037 157 GALLICNGYKDRDYIETAILGRRLGKTPILVIEQLEEVDVAIAASQRLGIEPILGVRAKLNARGMGRWG 225
********************************************************************* PP
TIGR01273 207 ssgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvk 275
ss+G+++KFGL++ +++++v+kl++++ll++l+llHfH+Gsqi++i+ +k++++Eaa++yv+l lG++
lcl|FitnessBrowser__SynE:Synpcc7942_1037 226 SSAGDRAKFGLTMPEIVAAVEKLQAANLLHCLQLLHFHIGSQISDISVLKDAIQEAAQIYVQLAALGAD 294
********************************************************************* PP
TIGR01273 276 ievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavl 344
++++dvGGGLgvdYdG+k + + s nY+++ ya++vva++k++c+++ + P++ sEsGRai++h +vl
lcl|FitnessBrowser__SynE:Synpcc7942_1037 295 MRYLDVGGGLGVDYDGSKTNFHASKNYNMQTYANDVVATIKDACQAHRLAVPTLTSESGRAIASHQSVL 363
********************************************************************* PP
TIGR01273 345 vaevleveeeeeeeaeeileeeapeevkeleellkeideesaeelledavqlleeavelfklGkldlee 413
v++vl+ +e ++ +e +ee +++v++l e+l++i e+++e+++da++l+e+av++f+lG+l+l+e
lcl|FitnessBrowser__SynE:Synpcc7942_1037 364 VFDVLGSSEVPRAAVEP-PQEEDSAIVRTLYEVLEAIALENLQECYHDAFKLKEDAVSAFRLGYLSLTE 431
********999996655.5559999******************************************** PP
TIGR01273 414 ralaeqlalailkkvkeleakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPlerLd 482
ra ae+l+ + +++++e+ ++ + e l++l+ +a+ y+vnls+Fqs PD+W+idqlfPi+P++rL+
lcl|FitnessBrowser__SynE:Synpcc7942_1037 432 RAKAERLFWSCCHRIQEFLKQLDRIPEDLEDLERVMASIYYVNLSVFQSAPDTWAIDQLFPIMPIHRLN 500
*****************77888888888999************************************** PP
TIGR01273 483 ekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdte 551
e+p++r +l+DltCDsDGki++f++ + ++tl lh+l++d++y+lg+fl GAYqEi+g+ HnLFgdt+
lcl|FitnessBrowser__SynE:Synpcc7942_1037 501 EEPNQRVTLADLTCDSDGKIDRFIDLLDVKSTLELHSLQPDQPYVLGMFLGGAYQEIMGNLHNLFGDTN 569
********************************************************************* PP
TIGR01273 552 avevvvkekgeveveaieegdtvedvlkavqydpeellkalkqk....vaeaklkaeekkqvlelleag 616
av++ ++ kg +++e++++gdt+ +vl +vqyd+e+ll++l+q+ ++ +++ +e++++l +e+g
lcl|FitnessBrowser__SynE:Synpcc7942_1037 570 AVHIKLTPKG-YSIEHVVKGDTMGEVLGYVQYDTEQLLERLRQQteaaLQQDQISLDEAQRLLRHYEEG 637
*********9.********************************988776777899************** PP
TIGR01273 617 lsgypYLs 624
l++y+YLs
lcl|FitnessBrowser__SynE:Synpcc7942_1037 638 LQRYTYLS 645
******96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (624 nodes)
Target sequences: 1 (647 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.61
//
[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