Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate AO353_13720 AO353_13720 arginine decarboxylase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1296 (637 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 AO353_13720 arginine decarboxylase Length = 637 Score = 1250 bits (3234), Expect = 0.0 Identities = 625/637 (98%), Positives = 633/637 (99%) Query: 1 MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60 MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAI+DAGRVEVRPNGP+S+PIDLFEQV Sbjct: 1 MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAISDAGRVEVRPNGPSSAPIDLFEQVA 60 Query: 61 QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120 QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN Sbjct: 61 QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120 Query: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI Sbjct: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180 Query: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF Sbjct: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 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+NKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL Sbjct: 361 DVEKHNDDVPMIENKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420 Query: 421 TLAQKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480 TLA+KALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA Sbjct: 421 TLAEKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480 Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540 IGQVLPILPLHRLDEEP+RRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLN+GEDYLL Sbjct: 481 IGQVLPILPLHRLDEEPMRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNDGEDYLL 540 Query: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL Sbjct: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600 Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637 MTHYRDK ASARISA ERTQ+LDALRLGLTRSSYLSS Sbjct: 601 MTHYRDKVASARISATERTQYLDALRLGLTRSSYLSS 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: 1415 Number of extensions: 44 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 AO353_13720 AO353_13720 (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.31577.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-271 887.7 0.0 2.5e-271 887.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 AO353_13720 arginine decarboxyla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 AO353_13720 arginine decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 887.5 0.0 2.5e-271 2.5e-271 1 624 [] 14 636 .. 14 636 .. 0.99 Alignments for each domain: == domain 1 score: 887.5 bits; conditional E-value: 2.5e-271 TIGR01273 1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpd 65 w++++s++vY+i++Wgagyfa+ ++G+v+vrp+g + ++ idl e v q+++ gl+lPllvrFpd lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 14 WTVADSRSVYGIRHWGAGYFAISDAGRVEVRPNGPS-SAPIDLFEQVAQLRKSGLSLPLLVRFPD 77 88999***************************9888.99************************** PP TIGR01273 66 ilqkrikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllia 130 ilq+r+++l+ aF+++ie+leY+sky+a+yPiKvnqq++v+e+++a+++ s+GLEaGsKpEll++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 78 ILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIENIIATQNVSIGLEAGSKPELLAV 142 ***************************************************************** PP TIGR01273 131 lalaekpkavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRv 195 lala ++ +ivcnGyKDre+i+lal+++klg++v+iviek++E+ lvieea++l+vkP++GlRv lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 143 LALAP-KGGTIVCNGYKDREFIRLALMGQKLGHNVFIVIEKESEVGLVIEEAASLKVKPQVGLRV 206 *****.8899******************************************************* PP TIGR01273 196 rLaskgsgkwassgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvr 260 rL+s +s+kwa++gGeksKFGLsa+q+l+vv+++++++l++ ++llHfH+Gsqian++d+++g++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 207 RLSSLASSKWADTGGEKSKFGLSAAQLLSVVERFRAAGLDQGIRLLHFHMGSQIANLADYQHGFK 271 ***************************************************************** PP TIGR01273 261 EaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvp 325 Ea+r+y elr+lG++++++dvGGGLgvdYdGt+s++++s+nY++++ya vv +lke+c+++++p lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 272 EAIRYYGELRNLGLPVDHIDVGGGLGVDYDGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLP 336 ***************************************************************** PP TIGR01273 326 ePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevkeleellkeideesaeell 390 +P+i+sEsGR++tahha+lv++v++ve+++++ +ee pe+v++l +ll+++d e+++e++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 337 HPNIFSESGRSLTAHHAMLVVQVTDVEKHNDDVPMIENKEELPETVQWLVDLLGPTDIEMVTETY 401 ******************************99633334489************************ PP TIGR01273 391 edavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaekyl 454 ++a+++++++++++++Gkl+l+e+alaeq++ a+++++++ l+a+++shr++ldel++kla+ky+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 402 WRATHYMSDVATQYADGKLTLAEKALAEQCYFAVCRRLHNsLKARQRSHRQVLDELNDKLADKYI 466 ***************************************************************** PP TIGR01273 455 vnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplhe 519 +n+s+FqslPD+W+i+q++PilPl+rLde+p rravl+DltCDsDGkik++v+eq+ie++lp+h lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 467 CNFSVFQSLPDTWAIGQVLPILPLHRLDEEPMRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHG 531 ***************************************************************** PP TIGR01273 520 ldkdeeyllgfflvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqyd 584 l+ e+yllg+flvGAYqEiLgd+HnLFgdt++v+++++++g+v+++ ie++dt+ed+l++v+++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 532 LNDGEDYLLGIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLS 596 ***************************************************************** PP TIGR01273 585 peellkalkqkvaeaklkaeekkqvlelleaglsgypYLs 624 peel++++++kva+a+++a e++q+l++l+ gl++++YLs lcl|FitnessBrowser__pseudo3_N2E3:AO353_13720 597 PEELMTHYRDKVASARISATERTQYLDALRLGLTRSSYLS 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 9.33 // [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