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.2496.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 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 10.49
//
[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