Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate N515DRAFT_3000 N515DRAFT_3000 arginine decarboxylase
Query= BRENDA::A0A0H2ZHZ8
(636 letters)
>FitnessBrowser__Dyella79:N515DRAFT_3000
Length = 629
Score = 593 bits (1529), Expect = e-174
Identities = 305/627 (48%), Positives = 411/627 (65%), Gaps = 8/627 (1%)
Query: 13 NWTVADSRGVYGIRHWGAGYFAINDGGNVEVRPQGADSTPIDLYELVGQLREAGLSLPLL 72
+W +R Y + HWG GY ++ G++ +RP+GA + L E+V + R GL LPLL
Sbjct: 4 HWNADAARHTYAVPHWGDGYVDVDARGHIVMRPRGAGGPALSLPEIVERARAEGLRLPLL 63
Query: 73 VRFPDILQDRVRKLTGAFDANIERLEYQSRYTALYPIKVNQQEAVVENIIATENVSIGLE 132
VRFPDIL DR+ +L GAF Y YTA+YPIKVNQQ V ++A GLE
Sbjct: 64 VRFPDILADRLARLQGAFAKATAEWNYGGGYTAVYPIKVNQQRGVAGELVAAGEHGFGLE 123
Query: 133 AGSKPELMAVLALAPKGGTIVCNGYKDREFIKLALMGQKLGHNVFIVIEKESEVQLVIEE 192
AGSKPELMAVLA+A G +VCNGYKDRE+++LAL+G+KLG V IVIEK SE+ V E
Sbjct: 124 AGSKPELMAVLAMARPGSIVVCNGYKDREYVRLALIGRKLGLRVHIVIEKLSELDHVFAE 183
Query: 193 AANVGVQPQVGLRVRLSSLASSKWADTGGEKAKFGLSAAQLLSVVERFRQAGLDQGVRLL 252
A +GV+P +G+RVRL+S+ + KW +TGG+K KFGLS Q+L++V R +AGL ++L
Sbjct: 184 AKALGVEPLLGVRVRLASIGAGKWQNTGGDKGKFGLSPNQVLTLVRRLDEAGLKHTLKLQ 243
Query: 253 HFHMGSQIANLADYQHGFKEAIRYYGELRALGLPVDHIDVGGGLGVDYDGTHSRNASSIN 312
HFHMGSQI+N+ D G +EA RYY EL +G+P++ +DVGGGLGVDY+G+ SR+ +SIN
Sbjct: 244 HFHMGSQISNVRDIAAGMREATRYYVELIRMGVPLEIVDVGGGLGVDYEGSRSRSHNSIN 303
Query: 313 YDIDDYAGVVVGMLKEFCDAQGLPHPHIFSESGRALTAHHAVLITQVTDVERHNDDVPKI 372
Y I+ YA +V L E +GL PHI +E+GRA+TAHHAV++ VT+VE +VP
Sbjct: 304 YSIEQYASTIVQSLAEAVAEEGLAAPHIVTEAGRAMTAHHAVMVVNVTEVE----EVPAG 359
Query: 373 V---DLDEQPEIVRWLAELLGPTDAEMVTETYWRATHYIGDAAAQYADGKISLAQKALAE 429
+++P ++R L E DA E + A H++ + YA G+++L +A +
Sbjct: 360 AIPPPREDEPAVLRRLRETYEELDARPALELFHEAQHHLNEGQTLYALGQLALEDRARLD 419
Query: 430 QCYFAICRRLHNQLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWAIGQVLPILP 489
+ Y+AI + +L +RSHRQ LDEL++KL DKY NFSVF+S+PD WAI Q+ PI P
Sbjct: 420 EMYYAIANAVRVRLLPAERSHRQALDELDEKLVDKYFVNFSVFESVPDIWAIDQIFPIAP 479
Query: 490 LHRLGEEPDRRAVLQDLTCDSDGKITQYVDEQSIETSLPVHEVKEGEDYLIGVFLVGAYQ 549
+ RL E P RR V+ DLTCDSDG+I YVD + ++ SLP+H V+EGE Y +G+F+VGAYQ
Sbjct: 480 IARLDEAPTRRGVIVDLTCDSDGRIDHYVDAEGVDVSLPLHAVREGESYRLGIFMVGAYQ 539
Query: 550 EILGDMHNLFGDTDSVNVYQRADGGIYHAGIETHDTIEDMLRYVHLSPEELMTLYRDKVA 609
E LGD+HNLFGDTD+VNV D ++ A DT + ML YV E L YR+++A
Sbjct: 540 ETLGDIHNLFGDTDAVNVRVEGDSYVF-AHRRRGDTTDLMLDYVGYDLEALRQSYRERIA 598
Query: 610 GAKLTARERNQYLDALRLGLTRSAYLS 636
A + Q L GLT YLS
Sbjct: 599 AAGVEGASAEQLFVTLNDGLTGYTYLS 625
Lambda K H
0.319 0.137 0.401
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: 1047
Number of extensions: 38
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: 636
Length of database: 629
Length adjustment: 38
Effective length of query: 598
Effective length of database: 591
Effective search space: 353418
Effective search space used: 353418
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 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate N515DRAFT_3000 N515DRAFT_3000 (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.7173.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.3e-251 821.0 0.0 3.8e-251 820.9 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 N515DRAFT_3000 arginine decarbox
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 N515DRAFT_3000 arginine decarboxylase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 820.9 0.0 3.8e-251 3.8e-251 1 624 [] 5 625 .. 5 625 .. 0.99
Alignments for each domain:
== domain 1 score: 820.9 bits; conditional E-value: 3.8e-251
TIGR01273 1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdi 66
w+a+ ++++Y + +Wg+gy++v+++G++++rp+g+ +l+e+v++++a+gl+lPllvrFpdi
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 5 WNADAARHTYAVPHWGDGYVDVDARGHIVMRPRGAG-GPALSLPEIVERARAEGLRLPLLVRFPDI 69
788999**************************9988.899************************** PP
TIGR01273 67 lqkrikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpElliala 132
l +r+++l+ aF++a e++Y + y+avyPiKvnqqr v elva g++ +GLEaGsKpEl+++la
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 70 LADRLARLQGAFAKATAEWNYGGGYTAVYPIKVNQQRGVAGELVAAGEHGFGLEAGSKPELMAVLA 135
****************************************************************** PP
TIGR01273 133 laekpkavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLa 198
+a+ p++++vcnGyKDrey++lali+rklgl v iviekl+Eld v +eak lgv+P lG+RvrLa
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 136 MAR-PGSIVVCNGYKDREYVRLALIGRKLGLRVHIVIEKLSELDHVFAEAKALGVEPLLGVRVRLA 200
**9.************************************************************** PP
TIGR01273 199 skgsgkwassgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaar 264
s g+gkw+++gG+k+KFGLs +qvl++v++l e++l+++lkl HfH+Gsqi+n++d++ g+rEa+r
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 201 SIGAGKWQNTGGDKGKFGLSPNQVLTLVRRLDEAGLKHTLKLQHFHMGSQISNVRDIAAGMREATR 266
****************************************************************** PP
TIGR01273 265 lyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePvii 330
+yvel ++Gv++e+vdvGGGLgvdY+G++s+s++s+nYs+e+ya+++v++l+e++ e+g+ P+i+
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 267 YYVELIRMGVPLEIVDVGGGLGVDYEGSRSRSHNSINYSIEQYASTIVQSLAEAVAEEGLAAPHIV 332
****************************************************************** PP
TIGR01273 331 sEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevkeleellkeideesaeelledavql 396
+E+GRa+tahhav+v++v+evee ++ ++ + e ++p+++++l+e ++e+d++ a el+++a+++
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 333 TEAGRAMTAHHAVMVVNVTEVEEVPAGAIPPPRE-DEPAVLRRLRETYEELDARPALELFHEAQHH 397
***************************8888766.9****************************** PP
TIGR01273 397 leeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekylvnlslFq 461
l+e +l++lG+l le+ra+ +++++ai ++v+ l e+shr+ ldel+ekl++ky+vn+s+F+
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 398 LNEGQTLYALGQLALEDRARLDEMYYAIANAVRVrLLPAERSHRQALDELDEKLVDKYFVNFSVFE 463
********************************999******************************* PP
TIGR01273 462 slPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyl 527
s+PD+W+idq+fPi P+ rLde+p+rr+v++DltCDsDG+i+++v+ +g + +lplh++++ e+y+
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 464 SVPDIWAIDQIFPIAPIARLDEAPTRRGVIVDLTCDSDGRIDHYVDAEGVDVSLPLHAVREGESYR 529
****************************************************************** PP
TIGR01273 528 lgfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalk 593
lg+f+vGAYqE Lgd+HnLFgdt+av+v v++++ + ++ ++gdt++ +l++v yd e l+++++
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 530 LGIFMVGAYQETLGDIHNLFGDTDAVNVRVEGDS-YVFAHRRRGDTTDLMLDYVGYDLEALRQSYR 594
******************************9998.899999************************* PP
TIGR01273 594 qkvaeaklkaeekkqvlelleaglsgypYLs 624
+++a+a ++ ++++q+ +l+ gl+gy+YLs
lcl|FitnessBrowser__Dyella79:N515DRAFT_3000 595 ERIAAAGVEGASAEQLFVTLNDGLTGYTYLS 625
*****************************96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (624 nodes)
Target sequences: 1 (629 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: 7.60
//
[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