Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 6939240 Sama_3334 ornithine decarboxylase (RefSeq)
Query= BRENDA::A4Q8H0
(720 letters)
>FitnessBrowser__SB2B:6939240
Length = 720
Score = 1140 bits (2948), Expect = 0.0
Identities = 540/718 (75%), Positives = 617/718 (85%)
Query: 1 MKKLKIAANEKTLGCFETEREIVDVHQSDFNDVAAIVLSVEDVAKGMVTHLEEIGLNIPL 60
M LKIAA+ CF+T+RE+V+V +DF DV A V+SV DV G+V ++ GLN+P+
Sbjct: 1 MNSLKIAASLSVRACFDTKREVVNVLTTDFCDVGAAVVSVTDVNNGIVDKIKNTGLNLPI 60
Query: 61 FVAVCCEEELDNAVLPALHGVFELCGKNTQFYGKQLEAAAVKYEKDLLPPFFNTLTQYVE 120
FV+VCCEE + + GVFELC T FYGKQ+E A +Y++ LLPPFF TL +YVE
Sbjct: 61 FVSVCCEEAFPDDFCDTITGVFELCNAKTDFYGKQVETAVRRYQESLLPPFFGTLKKYVE 120
Query: 121 MGNATFACPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCNADVKLGDLLIHEGLPCAAQ 180
MGN+TFACPGHQGG+FFRKHP GRQFFDF+GET+FRSDMCNADVKLGDLLIHEG P AQ
Sbjct: 121 MGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETVFRSDMCNADVKLGDLLIHEGAPHDAQ 180
Query: 181 QHAAKVFNADKTYFVLNGTSASNKVATNALLTRGDLVLFDRNNHKSNHHGALIQAGATPV 240
+AAKV+NADKTYFVLNGTSASNKV NALL GDLVLFDRNNHKSNHHGALIQAGATPV
Sbjct: 181 AYAAKVYNADKTYFVLNGTSASNKVVCNALLAPGDLVLFDRNNHKSNHHGALIQAGATPV 240
Query: 241 YLETARNPFGFIGGIDAHCFDERYLRQQIREVAPERANEARPFRLAIIQLGTYDGTIYNA 300
YLETARNPFGFIGGID+HCFDE YLR +I +VAPER ARPFRLAIIQLGTYDGTIYNA
Sbjct: 241 YLETARNPFGFIGGIDSHCFDEAYLRDEIGKVAPERVQAARPFRLAIIQLGTYDGTIYNA 300
Query: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELNENDPGIIVTQSVHKQQAGF 360
RQVVD+IGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLEL DPGIIVTQSVHKQQAGF
Sbjct: 301 RQVVDRIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELGAEDPGIIVTQSVHKQQAGF 360
Query: 361 SQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHASTSPFYPLFAALDVNAKMHEGKSGQRL 420
SQTSQIHKKD HIKGQ RYCNHKRFNNAFM+HASTSPFYPLFAALDVNAKMHEG SG+ L
Sbjct: 361 SQTSQIHKKDSHIKGQERYCNHKRFNNAFMMHASTSPFYPLFAALDVNAKMHEGASGRYL 420
Query: 421 WKECVRVGIEARKMLLETCQLIKPFVPDQIDGKPWQSYDTETMANDLRFFNFVPGEKWHA 480
W+E V+ GIEARK+LL+ C+ IKPF+P ++G+PWQS+DTE MA+DLRFF F PG KWHA
Sbjct: 421 WREAVKAGIEARKLLLKKCKYIKPFIPTTVEGEPWQSFDTERMADDLRFFEFEPGLKWHA 480
Query: 481 FEGYAESQYFVDPCKLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSIL 540
F+GY + QYFVDPCK LLTTPGI+ +G Y DFGIPATILAN+LREN I+PEKCDLNSIL
Sbjct: 481 FDGYEKGQYFVDPCKFLLTTPGINAETGEYEDFGIPATILANFLRENNIIPEKCDLNSIL 540
Query: 541 FLLTPAEDIAKMQHLVALIARFEKHIEQDSLLSEVLPAVYKSNEQRYKNYTLRQLCQEMH 600
FL+TPAED+AKMQHLV IARFEK I++D+ LSEVLP VY++N +RY+ Y++R+LCQEMH
Sbjct: 541 FLMTPAEDMAKMQHLVTQIARFEKLIDEDAPLSEVLPNVYRTNRERYEGYSIRRLCQEMH 600
Query: 601 DLYVSYDVKELQKEMFRKNYFPRIAMNPQDANTEFVRGNIELVSLAKAEGRIAAEGALPY 660
DLYVS +VK+LQKEMFR +FP+ MNPQDAN FVRG ELV L++ EG+IAAEGALPY
Sbjct: 601 DLYVSRNVKQLQKEMFRAAHFPKAVMNPQDANIAFVRGKAELVPLSEIEGQIAAEGALPY 660
Query: 661 PPGVLCVVPGEIWGGAAQRYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYVM 718
PPGVLC+VPGE+WGGA QRYFLALEEGINLLPGFAPELQGVY+++ ++G +A GYV+
Sbjct: 661 PPGVLCMVPGEVWGGAVQRYFLALEEGINLLPGFAPELQGVYLERADNGRVQAMGYVL 718
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: 1641
Number of extensions: 58
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: 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 6939240 Sama_3334 (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.4938.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 1409.3 0.0 0 1409.2 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6939240 Sama_3334 ornithine decarboxylas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939240 Sama_3334 ornithine decarboxylase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1409.2 0.0 0 0 1 719 [] 1 719 [. 1 719 [. 1.00
Alignments for each domain:
== domain 1 score: 1409.2 bits; conditional E-value: 0
TIGR04301 1 mkklkiavsesvkdafeterevveleetdftdvaavvlsvedvkagvlekieetafeipvfvvveeeekvsaellkk 77
m++lkia+s sv+ +f+t+revv++ +tdf+dv+a+v+sv dv++g+++ki++t++++p+fv v++ee ++++ +++
lcl|FitnessBrowser__SB2B:6939240 1 MNSLKIAASLSVRACFDTKREVVNVLTTDFCDVGAAVVSVTDVNNGIVDKIKNTGLNLPIFVSVCCEEAFPDDFCDT 77
899************************************************************************** PP
TIGR04301 78 vtgvidleekdaelygrqleeaakkyeekllppffkalkkyvekgnsafdcpghqggeffrkhpagrqfvdffgenl 154
+tgv++l++ ++++yg+q+e+a+++y+e+llppff++lkkyve+gns+f+cpghqgg+ffrkhp+grqf+dffge++
lcl|FitnessBrowser__SB2B:6939240 78 ITGVFELCNAKTDFYGKQVETAVRRYQESLLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETV 154
***************************************************************************** PP
TIGR04301 155 frsdlcnadvalgdllihegaplaaqkhaakvfnadktyfvlngtsasnkvvlnallapgdlvlfdrnnhksnhhga 231
frsd+cnadv+lgdllihegap++aq +aakv+nadktyfvlngtsasnkvv+nallapgdlvlfdrnnhksnhhga
lcl|FitnessBrowser__SB2B:6939240 155 FRSDMCNADVKLGDLLIHEGAPHDAQAYAAKVYNADKTYFVLNGTSASNKVVCNALLAPGDLVLFDRNNHKSNHHGA 231
***************************************************************************** PP
TIGR04301 232 llqagatpvyletarnpfgfiggidehcfeeeylrelirevaperakekrpfrlaviqlgtydgtiynarqvvdkig 308
l+qagatpvyletarnpfgfiggid+hcf+e+ylr+ i +vaper++++rpfrla+iqlgtydgtiynarqvvd+ig
lcl|FitnessBrowser__SB2B:6939240 232 LIQAGATPVYLETARNPFGFIGGIDSHCFDEAYLRDEIGKVAPERVQAARPFRLAIIQLGTYDGTIYNARQVVDRIG 308
***************************************************************************** PP
TIGR04301 309 hlcdyilfdsawvgyeqfipmmkdcsplllelneedpgilvtqsvhkqqagfsqtsqihkkdkhikgqaryvnhkrl 385
hlcdyilfdsawvgyeqfipmmkdcsplllel+ edpgi+vtqsvhkqqagfsqtsqihkkd+hikgq+ry+nhkr+
lcl|FitnessBrowser__SB2B:6939240 309 HLCDYILFDSAWVGYEQFIPMMKDCSPLLLELGAEDPGIIVTQSVHKQQAGFSQTSQIHKKDSHIKGQERYCNHKRF 385
***************************************************************************** PP
TIGR04301 386 nnafmlhastspfyplfaaldvnaklhegeagkrlwadcvktgiearklllkscklikpfvpelvdgkkwedydtee 462
nnafm+hastspfyplfaaldvnak+heg++g+ lw+++vk+giearklllk+ck+ikpf+p++v+g++w+++dte+
lcl|FitnessBrowser__SB2B:6939240 386 NNAFMMHASTSPFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCKYIKPFIPTTVEGEPWQSFDTER 462
***************************************************************************** PP
TIGR04301 463 iandlrffefepgekwhsfegyeeeqyfvdpcklllttpgidvetgeyeefgvpatilanflrengiipekcdlnsi 539
+a+dlrffefepg kwh+f+gye+ qyfvdpck+llttpgi++etgeye+fg+patilanflren+iipekcdlnsi
lcl|FitnessBrowser__SB2B:6939240 463 MADDLRFFEFEPGLKWHAFDGYEKGQYFVDPCKFLLTTPGINAETGEYEDFGIPATILANFLRENNIIPEKCDLNSI 539
***************************************************************************** PP
TIGR04301 540 lflltpaedlaklqelvaqiarfeklleedaplkevlpsvykaneerykgytirqlcqemhdlykernvkqlqkelf 616
lfl+tpaed+ak+q+lv+qiarfekl++edapl+evlp+vy++n+ery+gy+ir+lcqemhdly++rnvkqlqke+f
lcl|FitnessBrowser__SB2B:6939240 540 LFLMTPAEDMAKMQHLVTQIARFEKLIDEDAPLSEVLPNVYRTNRERYEGYSIRRLCQEMHDLYVSRNVKQLQKEMF 616
***************************************************************************** PP
TIGR04301 617 rkeylpkvvlnpqeanleflrgevelveleeaegriaaegalpyppgvlcvvpgevwggavlkyflaleeginllpg 693
r +++pk+v+npq+an++f+rg++elv+l+e+eg+iaaegalpyppgvlc+vpgevwggav++yflaleeginllpg
lcl|FitnessBrowser__SB2B:6939240 617 RAAHFPKAVMNPQDANIAFVRGKAELVPLSEIEGQIAAEGALPYPPGVLCMVPGEVWGGAVQRYFLALEEGINLLPG 693
***************************************************************************** PP
TIGR04301 694 fapelqgvyleededgrkraygyvlk 719
fapelqgvyle++ +gr +a gyvlk
lcl|FitnessBrowser__SB2B:6939240 694 FAPELQGVYLERADNGRVQAMGYVLK 719
************************97 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: 10.78
//
[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