Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate GFF591 PS417_03005 arginine decarboxylase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1296 (637 letters) >FitnessBrowser__WCS417:GFF591 Length = 637 Score = 1243 bits (3217), Expect = 0.0 Identities = 621/637 (97%), Positives = 630/637 (98%) Query: 1 MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60 MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGP S+P+DL+EQVD Sbjct: 1 MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPNSTPVDLYEQVD 60 Query: 61 QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120 +LRKSGLSLPLLVRFPDILQDRVRQLTGAFD+NIERLEYQSKYTALYPIKVNQQEAVIEN Sbjct: 61 ELRKSGLSLPLLVRFPDILQDRVRQLTGAFDSNIERLEYQSKYTALYPIKVNQQEAVIEN 120 Query: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI Sbjct: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180 Query: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240 EKESEV LVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF Sbjct: 181 EKESEVELVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240 Query: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY Sbjct: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300 Query: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT Sbjct: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360 Query: 361 DVEKHNDDVPKIDNKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420 DVEKHNDDVP I+NKE LPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL Sbjct: 361 DVEKHNDDVPVIENKEALPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420 Query: 421 TLAQKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480 TLA+KALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA Sbjct: 421 TLAEKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480 Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL Sbjct: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540 Query: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600 GIFLVGAYQEILGDMHNLFGDTDSVNIYQ DGSVY AGIETHDTIEDMLRYVHLSPEEL Sbjct: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQREDGSVYSAGIETHDTIEDMLRYVHLSPEEL 600 Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637 MTHYRDKCASA+ISA+ERTQFLDALRLGLTRSSYLSS Sbjct: 601 MTHYRDKCASAKISASERTQFLDALRLGLTRSSYLSS 637 Lambda K H 0.319 0.136 0.396 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: 1407 Number of extensions: 47 Number of successful extensions: 1 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: 637 Length of database: 637 Length adjustment: 38 Effective length of query: 599 Effective length of database: 599 Effective search space: 358801 Effective search space used: 358801 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 GFF591 PS417_03005 (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.2090.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-273 892.2 0.0 1.1e-272 892.0 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF591 PS417_03005 arginine decarboxyla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF591 PS417_03005 arginine decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 892.0 0.0 1.1e-272 1.1e-272 1 624 [] 14 636 .. 14 636 .. 0.99 Alignments for each domain: == domain 1 score: 892.0 bits; conditional E-value: 1.1e-272 TIGR01273 1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslna 76 w++++s++vY+i++Wgagyfa+n++G+v+vrp+g + ++ +dl+e v+++++ gl+lPllvrFpdilq+r+++l+ lcl|FitnessBrowser__WCS417:GFF591 14 WTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPN-STPVDLYEQVDELRKSGLSLPLLVRFPDILQDRVRQLTG 88 88999****************************999.99************************************* PP TIGR01273 77 aFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpkavivcnGyKDreyi 152 aF+++ie+leY+sky+a+yPiKvnqq++v+e+++a+++ s+GLEaGsKpEll++lala ++ +ivcnGyKDre+i lcl|FitnessBrowser__WCS417:GFF591 89 AFDSNIERLEYQSKYTALYPIKVNQQEAVIENIIATQNVSIGLEAGSKPELLAVLALAP-KGGTIVCNGYKDREFI 163 ***********************************************************.8899************ PP TIGR01273 153 elaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvkk 228 +lal+++klg++v+iviek++E++lvieea++l+vkP++GlRvrL+s +s+kwa++gGeksKFGLsa+q+l+vv++ lcl|FitnessBrowser__WCS417:GFF591 164 RLALMGQKLGHNVFIVIEKESEVELVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVER 239 **************************************************************************** PP TIGR01273 229 lkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsl 304 +++++l++ ++llHfH+Gsqian++d+++g++Ea+r+y elr+lG++++++dvGGGLgvdYdGt+s++++s+nY++ lcl|FitnessBrowser__WCS417:GFF591 240 FRAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDYDGTHSRNASSINYDM 315 **************************************************************************** PP TIGR01273 305 eeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeee.aeeileeeapeevkeleellk 379 ++ya vv +lke+c+++++p+P+i+sEsGR++tahha+lv++v++ve+++++ + e +e+ pe+v++l +ll+ lcl|FitnessBrowser__WCS417:GFF591 316 DDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVTDVEKHNDDVpVIE-NKEALPETVQWLVDLLG 390 ***************************************************9963333.4479************* PP TIGR01273 380 eideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekyl 454 ++d e+++e++++a+++++++++++++Gkl+l+e+alaeq++ a+++++++ l+a+++shr++ldel++kla+ky+ lcl|FitnessBrowser__WCS417:GFF591 391 PTDIEMVTETYWRATHYMSDVATQYADGKLTLAEKALAEQCYFAVCRRLHNsLKARQRSHRQVLDELNDKLADKYI 466 **************************************************************************** PP TIGR01273 455 vnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgf 530 +n+s+FqslPD+W+i+q++PilPl+rLde+p rravl+DltCDsDGkik++v+eq+ie++lp+h l++ e+yllg+ lcl|FitnessBrowser__WCS417:GFF591 467 CNFSVFQSLPDTWAIGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLLGI 542 **************************************************************************** PP TIGR01273 531 flvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeek 606 flvGAYqEiLgd+HnLFgdt++v+++++e+g+v+ + ie++dt+ed+l++v+++peel++++++k a+ak++a+e+ lcl|FitnessBrowser__WCS417:GFF591 543 FLVGAYQEILGDMHNLFGDTDSVNIYQREDGSVYSAGIETHDTIEDMLRYVHLSPEELMTHYRDKCASAKISASER 618 **************************************************************************** PP TIGR01273 607 kqvlelleaglsgypYLs 624 +q+l++l+ gl++++YLs lcl|FitnessBrowser__WCS417:GFF591 619 TQFLDALRLGLTRSSYLS 636 ****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (624 nodes) Target sequences: 1 (637 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 10.35 // [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