Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 7026738 Shewana3_3871 ornithine decarboxylase (RefSeq)
Query= BRENDA::A4Q8H0
(720 letters)
>FitnessBrowser__ANA3:7026738
Length = 720
Score = 1165 bits (3013), Expect = 0.0
Identities = 547/719 (76%), Positives = 630/719 (87%)
Query: 1 MKKLKIAANEKTLGCFETEREIVDVHQSDFNDVAAIVLSVEDVAKGMVTHLEEIGLNIPL 60
MK LK+AA+ CFE +RE+V+V +DF DV A V+SV+DV G+V ++ GL +P+
Sbjct: 1 MKSLKVAASLSVRSCFEIDREVVNVLTTDFCDVGAAVVSVDDVKNGIVEKIKNTGLKLPI 60
Query: 61 FVAVCCEEELDNAVLPALHGVFELCGKNTQFYGKQLEAAAVKYEKDLLPPFFNTLTQYVE 120
FV+VCCEE + + ++ GVFELCG NT FYGKQ+E A KYE+ LLPPFF TL +YVE
Sbjct: 61 FVSVCCEETFPDDICSSITGVFELCGSNTDFYGKQVETAVQKYEQALLPPFFGTLKKYVE 120
Query: 121 MGNATFACPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCNADVKLGDLLIHEGLPCAAQ 180
MGN+TFACPGHQGG+FFRKHP GRQFFDF+GET+FRSDMCNADVKLGDLLIHEG P AQ
Sbjct: 121 MGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETIFRSDMCNADVKLGDLLIHEGAPLDAQ 180
Query: 181 QHAAKVFNADKTYFVLNGTSASNKVATNALLTRGDLVLFDRNNHKSNHHGALIQAGATPV 240
++AAKVFNADKTYFVLNGTS+SNKVATNALL +GDLVLFDRNNHKSNHHGALIQAGATP+
Sbjct: 181 KYAAKVFNADKTYFVLNGTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGALIQAGATPI 240
Query: 241 YLETARNPFGFIGGIDAHCFDERYLRQQIREVAPERANEARPFRLAIIQLGTYDGTIYNA 300
YLETARNPFGFIGGIDAHCF E YLR+QIR VAPERA+E RPFRLAIIQLGTYDGTIYNA
Sbjct: 241 YLETARNPFGFIGGIDAHCFQESYLREQIRAVAPERADEQRPFRLAIIQLGTYDGTIYNA 300
Query: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELNENDPGIIVTQSVHKQQAGF 360
RQVVD+IGHLCDYILFDSAWVGYEQFIPMM DCSPLLLEL DPGIIVTQSVHKQQAGF
Sbjct: 301 RQVVDRIGHLCDYILFDSAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGF 360
Query: 361 SQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHASTSPFYPLFAALDVNAKMHEGKSGQRL 420
SQTSQIHKKD HIKGQ+RYCNHKRFNNAFM+HASTSPFYPLFAALDVNAKMHEG SG+ L
Sbjct: 361 SQTSQIHKKDSHIKGQARYCNHKRFNNAFMMHASTSPFYPLFAALDVNAKMHEGASGRYL 420
Query: 421 WKECVRVGIEARKMLLETCQLIKPFVPDQIDGKPWQSYDTETMANDLRFFNFVPGEKWHA 480
W+E V+ GIEARK+LL+ C+ IKPF+P I+G+PWQ Y TE MA+DLRFF F PG+KWH+
Sbjct: 421 WREAVKAGIEARKLLLKKCKYIKPFIPSMIEGRPWQDYPTEQMADDLRFFEFEPGQKWHS 480
Query: 481 FEGYAESQYFVDPCKLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSIL 540
F+GY + QYFVDPCK LLTTPGID +G Y++FGIPATILAN+LREN I+PEKCDLNSIL
Sbjct: 481 FDGYEKGQYFVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSIL 540
Query: 541 FLLTPAEDIAKMQHLVALIARFEKHIEQDSLLSEVLPAVYKSNEQRYKNYTLRQLCQEMH 600
FL+TPAED+AKMQHLV+ I+RFEK +++D+ LSEVLP VY +N+ RYK+YT+RQLCQEMH
Sbjct: 541 FLMTPAEDMAKMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMH 600
Query: 601 DLYVSYDVKELQKEMFRKNYFPRIAMNPQDANTEFVRGNIELVSLAKAEGRIAAEGALPY 660
+LYVS+DVK+LQKEMFR+ +FP M+PQ+AN EF+RG +ELV L++ EGRIAAEGALPY
Sbjct: 601 NLYVSHDVKQLQKEMFRQAHFPTKVMDPQEANLEFIRGKVELVPLSQIEGRIAAEGALPY 660
Query: 661 PPGVLCVVPGEIWGGAAQRYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYVMS 719
PPGVLCVVPGEIWGGA QRYFLALEEGINLLPGF+PELQGVY++ DG +A GYV++
Sbjct: 661 PPGVLCVVPGEIWGGAVQRYFLALEEGINLLPGFSPELQGVYLETPPDGKIQALGYVLN 719
Lambda K H
0.321 0.138 0.420
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: 1658
Number of extensions: 58
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: 720
Length of database: 720
Length adjustment: 40
Effective length of query: 680
Effective length of database: 680
Effective search space: 462400
Effective search space used: 462400
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 (21.9 bits)
S2: 55 (25.8 bits)
Align candidate 7026738 Shewana3_3871 (ornithine decarboxylase (RefSeq))
to HMM TIGR04301 (speF: ornithine decarboxylase SpeF (EC 4.1.1.17))
# 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/TIGR04301.hmm
# target sequence database: /tmp/gapView.29966.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR04301 [M=719]
Accession: TIGR04301
Description: ODC_inducible: ornithine decarboxylase SpeF
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1433.5 0.0 0 1433.4 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7026738 Shewana3_3871 ornithine decarbox
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026738 Shewana3_3871 ornithine decarboxylase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1433.4 0.0 0 0 1 719 [] 1 719 [. 1 719 [. 1.00
Alignments for each domain:
== domain 1 score: 1433.4 bits; conditional E-value: 0
TIGR04301 1 mkklkiavsesvkdafeterevveleetdftdvaavvlsvedvkagvlekieetafeipvfvvveeeekvsaellkk 77
mk+lk+a+s sv+++fe++revv++ +tdf+dv+a+v+sv+dvk+g++eki++t++++p+fv v++ee+++++++++
lcl|FitnessBrowser__ANA3:7026738 1 MKSLKVAASLSVRSCFEIDREVVNVLTTDFCDVGAAVVSVDDVKNGIVEKIKNTGLKLPIFVSVCCEETFPDDICSS 77
99*************************************************************************** PP
TIGR04301 78 vtgvidleekdaelygrqleeaakkyeekllppffkalkkyvekgnsafdcpghqggeffrkhpagrqfvdffgenl 154
+tgv++l+ +++++yg+q+e+a++kye++llppff++lkkyve+gns+f+cpghqgg+ffrkhp+grqf+dffge++
lcl|FitnessBrowser__ANA3:7026738 78 ITGVFELCGSNTDFYGKQVETAVQKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETI 154
***************************************************************************** PP
TIGR04301 155 frsdlcnadvalgdllihegaplaaqkhaakvfnadktyfvlngtsasnkvvlnallapgdlvlfdrnnhksnhhga 231
frsd+cnadv+lgdllihegapl+aqk+aakvfnadktyfvlngts+snkv++nalla+gdlvlfdrnnhksnhhga
lcl|FitnessBrowser__ANA3:7026738 155 FRSDMCNADVKLGDLLIHEGAPLDAQKYAAKVFNADKTYFVLNGTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGA 231
***************************************************************************** PP
TIGR04301 232 llqagatpvyletarnpfgfiggidehcfeeeylrelirevaperakekrpfrlaviqlgtydgtiynarqvvdkig 308
l+qagatp+yletarnpfgfiggid+hcf+e+ylre+ir+vapera+e+rpfrla+iqlgtydgtiynarqvvd+ig
lcl|FitnessBrowser__ANA3:7026738 232 LIQAGATPIYLETARNPFGFIGGIDAHCFQESYLREQIRAVAPERADEQRPFRLAIIQLGTYDGTIYNARQVVDRIG 308
***************************************************************************** PP
TIGR04301 309 hlcdyilfdsawvgyeqfipmmkdcsplllelneedpgilvtqsvhkqqagfsqtsqihkkdkhikgqaryvnhkrl 385
hlcdyilfdsawvgyeqfipmm+dcsplllel++edpgi+vtqsvhkqqagfsqtsqihkkd+hikgqary+nhkr+
lcl|FitnessBrowser__ANA3:7026738 309 HLCDYILFDSAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGFSQTSQIHKKDSHIKGQARYCNHKRF 385
***************************************************************************** PP
TIGR04301 386 nnafmlhastspfyplfaaldvnaklhegeagkrlwadcvktgiearklllkscklikpfvpelvdgkkwedydtee 462
nnafm+hastspfyplfaaldvnak+heg++g+ lw+++vk+giearklllk+ck+ikpf+p++++g++w+dy+te+
lcl|FitnessBrowser__ANA3:7026738 386 NNAFMMHASTSPFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCKYIKPFIPSMIEGRPWQDYPTEQ 462
***************************************************************************** PP
TIGR04301 463 iandlrffefepgekwhsfegyeeeqyfvdpcklllttpgidvetgeyeefgvpatilanflrengiipekcdlnsi 539
+a+dlrffefepg+kwhsf+gye+ qyfvdpck+llttpgid+etg+y+efg+patilanflren+iipekcdlnsi
lcl|FitnessBrowser__ANA3:7026738 463 MADDLRFFEFEPGQKWHSFDGYEKGQYFVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSI 539
***************************************************************************** PP
TIGR04301 540 lflltpaedlaklqelvaqiarfeklleedaplkevlpsvykaneerykgytirqlcqemhdlykernvkqlqkelf 616
lfl+tpaed+ak+q+lv+qi+rfekl++edapl+evlp+vy+an++ryk+ytirqlcqemh+ly++++vkqlqke+f
lcl|FitnessBrowser__ANA3:7026738 540 LFLMTPAEDMAKMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVKQLQKEMF 616
***************************************************************************** PP
TIGR04301 617 rkeylpkvvlnpqeanleflrgevelveleeaegriaaegalpyppgvlcvvpgevwggavlkyflaleeginllpg 693
r++++p++v++pqeanlef+rg+velv+l+++egriaaegalpyppgvlcvvpge+wggav++yflaleeginllpg
lcl|FitnessBrowser__ANA3:7026738 617 RQAHFPTKVMDPQEANLEFIRGKVELVPLSQIEGRIAAEGALPYPPGVLCVVPGEIWGGAVQRYFLALEEGINLLPG 693
***************************************************************************** PP
TIGR04301 694 fapelqgvyleededgrkraygyvlk 719
f+pelqgvyle+ dg+ +a gyvl+
lcl|FitnessBrowser__ANA3:7026738 694 FSPELQGVYLETPPDGKIQALGYVLN 719
************************95 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (719 nodes)
Target sequences: 1 (720 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 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.36
//
[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