Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 7024446 Shewana3_1624 arginine decarboxylase (RefSeq)
Query= BRENDA::Q7MK24 (640 letters) >FitnessBrowser__ANA3:7024446 Length = 637 Score = 891 bits (2302), Expect = 0.0 Identities = 436/631 (69%), Positives = 523/631 (82%), Gaps = 1/631 (0%) Query: 11 LDRVRADYNVHYWSQGFYGIDDQGEMYVSPRSDNA-HQIQLSKIVKQLEERQLNVPVLVR 69 +D RA YNV +WSQGFYGI DQGE+ VSP N H+I L+++ K + + + +PVLVR Sbjct: 6 IDAARAGYNVTHWSQGFYGISDQGEVTVSPDPKNPDHKIGLNELAKDMVKAGVALPVLVR 65 Query: 70 FPQILHQRVHSICDAFNQAIEEYQYPNKYLLVYPIKVNQQREVVDEILASQAQLETKQLG 129 FPQILH RV+S+C AF+QAI++Y+Y YLLVYPIKVNQQ+ VV+EILASQA E QLG Sbjct: 66 FPQILHHRVNSLCQAFDQAIQKYEYQADYLLVYPIKVNQQKTVVEEILASQASKEVPQLG 125 Query: 130 LEAGSKPELLAVLAMAQHASSVIVCNGYKDREYIRLALIGEKLGHKVFIVLEKMSELDLV 189 LEAGSKPEL+AVLAMAQ ASSVIVCNGYKD EYIRLALIGEKLGHKV+IVLEK+SEL +V Sbjct: 126 LEAGSKPELMAVLAMAQKASSVIVCNGYKDNEYIRLALIGEKLGHKVYIVLEKLSELKMV 185 Query: 190 LREAKSLGVTPRLGIRIRLASQGAGKWQASGGEKSKFGLSASQVLNVISRLKKENQLDTL 249 L E+K LGV PRLG+R RLA QG GKWQASGGEKSKFGLSA+Q+L V+ +LK+E+ LD+L Sbjct: 186 LAESKRLGVKPRLGLRARLAFQGKGKWQASGGEKSKFGLSAAQILTVVDQLKQEDMLDSL 245 Query: 250 QLVHFHLGSQMANIRDVRNGVNESARFYCELRTLGANITYFDVGGGLAIDYDGTRSQSSN 309 QL+HFHLGSQ+ANIRD+R GV+E+ARFYCELR LGA+I FDVGGGLA+DYDGTRSQS+N Sbjct: 246 QLLHFHLGSQIANIRDIRQGVSEAARFYCELRELGASINCFDVGGGLAVDYDGTRSQSNN 305 Query: 310 SMNYGLVEYARNIVNTVGDVCKDYKQPMPVIISESGRSLTAHHAVLISNVIGTETYKPET 369 SMNYGL EYA NIVN + D+C +Y+QPMP IISESGR LTAHHAVLI++VIGTE Y+ E Sbjct: 306 SMNYGLSEYANNIVNVLTDICNEYEQPMPRIISESGRHLTAHHAVLITDVIGTEAYQVEE 365 Query: 370 VTEPEEDFPLLLNNMWRSWLNLHNGTDARALIEIYNDTQSDLAEVHSQFATGVLTLEHRA 429 + P E+ P LL+NMW+SW + D RALIEIY+D+QSDL E S FA G L+L RA Sbjct: 366 IQPPAEESPQLLHNMWQSWTEISGRADQRALIEIYHDSQSDLQEAQSLFALGQLSLAERA 425 Query: 430 WAEQTSLRIYYELNRLMSTKNRFHRPILDELSERLADKFFVNFSLFQSLPDSWGIDQVFP 489 WAEQ +LR+ +E+ L+STKNR+HRPI+DEL+E+LADKFFVNFSLFQSLPD+WGIDQVFP Sbjct: 426 WAEQANLRVCHEVQGLLSTKNRYHRPIIDELNEKLADKFFVNFSLFQSLPDAWGIDQVFP 485 Query: 490 VLPLSGLQNAADRRAVMLDITCDSDGAIDAYVDGQGIESTLPVPAWNEDEPYLMGFFLVG 549 VLPLSGL A +RRAVMLDITCDSDG +D YVDGQGIE+TLPVPAW+ + PYLMGFF+VG Sbjct: 486 VLPLSGLDKAPERRAVMLDITCDSDGIVDQYVDGQGIETTLPVPAWSAESPYLMGFFMVG 545 Query: 550 AYQEILGDMHNLFGDTHSVVVNVGDQGEINIDFINEGDTVEDMMRYVHIDVDQIRKNYHS 609 AYQEILGDMHNLFGDT+S VV++ + G NI+ + GDTV D++RYV++D + Y Sbjct: 546 AYQEILGDMHNLFGDTNSAVVSIEENGMTNIESVLAGDTVADVLRYVNLDAVDFMRTYEE 605 Query: 610 LVSQRVDQEEQQQILAELEQGLSGYTYLEDF 640 LV+Q + +EE+ QIL EL+ GL GYTYLEDF Sbjct: 606 LVNQHIAEEERAQILEELQVGLKGYTYLEDF 636 Lambda K H 0.318 0.135 0.392 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: 1155 Number of extensions: 44 Number of successful extensions: 2 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: 640 Length of database: 637 Length adjustment: 38 Effective length of query: 602 Effective length of database: 599 Effective search space: 360598 Effective search space used: 360598 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 7024446 Shewana3_1624 (arginine decarboxylase (RefSeq))
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.30337.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-269 881.9 0.1 1.4e-269 881.7 0.1 1.0 1 lcl|FitnessBrowser__ANA3:7024446 Shewana3_1624 arginine decarboxy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024446 Shewana3_1624 arginine decarboxylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 881.7 0.1 1.4e-269 1.4e-269 1 624 [] 4 634 .. 4 634 .. 0.98 Alignments for each domain: == domain 1 score: 881.7 bits; conditional E-value: 1.4e-269 TIGR01273 1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaa 77 ws++ +++ Yn+++W++g++ + ++Gev+v+p+ ++ ++i l el k++ ++g+ lP+lvrFp+il++r++sl++a lcl|FitnessBrowser__ANA3:7024446 4 WSIDAARAGYNVTHWSQGFYGISDQGEVTVSPDPKNPDHKIGLNELAKDMVKAGVALPVLVRFPQILHHRVNSLCQA 80 78999999********************************************************************* PP TIGR01273 78 FkeaieeleYaskyqavyPiKvnqqrevveelvasg....gkslGLEaGsKpEllialalaekpkavivcnGyKDre 150 F++ai+++eY+++y +vyPiKvnqq++vvee++as+ +lGLEaGsKpEl+++la+a+k+++vivcnGyKD+e lcl|FitnessBrowser__ANA3:7024446 81 FDQAIQKYEYQADYLLVYPIKVNQQKTVVEEILASQaskeVPQLGLEAGSKPELMAVLAMAQKASSVIVCNGYKDNE 157 **********************************9986434589********************************* PP TIGR01273 151 yielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvk 227 yi+lali++klg+kv+iv+ekl+El++v++e+k+lgvkP+lGlR+rLa +g gkw+ sgGeksKFGLsa+q+l+vv+ lcl|FitnessBrowser__ANA3:7024446 158 YIRLALIGEKLGHKVYIVLEKLSELKMVLAESKRLGVKPRLGLRARLAFQGKGKWQASGGEKSKFGLSAAQILTVVD 234 ***************************************************************************** PP TIGR01273 228 klkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsl 304 +lk+ed+ldsl+llHfHlGsqiani+d+++gv+Eaar+y+elr+lG++i+++dvGGGL+vdYdGt+s+s++s+nY+l lcl|FitnessBrowser__ANA3:7024446 235 QLKQEDMLDSLQLLHFHLGSQIANIRDIRQGVSEAARFYCELRELGASINCFDVGGGLAVDYDGTRSQSNNSMNYGL 311 ***************************************************************************** PP TIGR01273 305 eeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevk....eleel 377 eya+++v +l ++c+e+++p P+iisEsGR +tahhavl+++v+++e+++ ee++ ++e e+p++++ +++e+ lcl|FitnessBrowser__ANA3:7024446 312 SEYANNIVNVLTDICNEYEQPMPRIISESGRHLTAHHAVLITDVIGTEAYQVEEIQPPAE-ESPQLLHnmwqSWTEI 387 ***************************************************998777666.99999998887899** PP TIGR01273 378 lkeideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaeky 453 ++ +d+++++e+++d++++l+ea +lf+lG+l+l+era+aeq l+++++v+ l++k++ hr+i+del+ekla+k+ lcl|FitnessBrowser__ANA3:7024446 388 SGRADQRALIEIYHDSQSDLQEAQSLFALGQLSLAERAWAEQANLRVCHEVQGlLSTKNRYHRPIIDELNEKLADKF 464 *****************************************************99********************** PP TIGR01273 454 lvnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgf 530 +vn+slFqslPDaWgidq+fP+lPl++Ld++p+rrav+lD+tCDsDG ++++v++qgie+tlp+++++ + +yl+gf lcl|FitnessBrowser__ANA3:7024446 465 FVNFSLFQSLPDAWGIDQVFPVLPLSGLDKAPERRAVMLDITCDSDGIVDQYVDGQGIETTLPVPAWSAESPYLMGF 541 ***************************************************************************** PP TIGR01273 531 flvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekk 607 f+vGAYqEiLgd+HnLFgdt+++ v ++e+g +++e++ gdtv+dvl++v++d+ + ++++++ v++ ++++ee++ lcl|FitnessBrowser__ANA3:7024446 542 FMVGAYQEILGDMHNLFGDTNSAVVSIEENGMTNIESVLAGDTVADVLRYVNLDAVDFMRTYEELVNQ-HIAEEERA 617 *****************************************************************998.59****** PP TIGR01273 608 qvlelleaglsgypYLs 624 q+le+l++gl+gy+YL+ lcl|FitnessBrowser__ANA3:7024446 618 QILEELQVGLKGYTYLE 634 ***************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 0.02s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 7.68 // [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