Alignments for a candidate for odc in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Shewanella oneidensis MR-1

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 199509 SO0314 ornithine decarboxylase, inducible (NCBI ptt file)

Query= BRENDA::A4Q8H0
         (720 letters)



>FitnessBrowser__MR1:199509
          Length = 720

 Score = 1164 bits (3010), Expect = 0.0
 Identities = 548/719 (76%), Positives = 630/719 (87%)

Query: 1   MKKLKIAANEKTLGCFETEREIVDVHQSDFNDVAAIVLSVEDVAKGMVTHLEEIGLNIPL 60
           MK LK+AA+     CF+ +RE+V+V  +DF DV A V+SV+DV  G+V  ++  GL +P+
Sbjct: 1   MKSLKVAASLSVRSCFDIDREVVNVLTTDFCDVGAAVVSVDDVKDGIVEKIKNTGLKLPI 60

Query: 61  FVAVCCEEELDNAVLPALHGVFELCGKNTQFYGKQLEAAAVKYEKDLLPPFFNTLTQYVE 120
           FV+VCCEE   + +  ++ GVFELCG NT FYGKQ+E A  KYE+ LLPPFF TL +YVE
Sbjct: 61  FVSVCCEETFPDDICSSITGVFELCGSNTDFYGKQVETAIKKYEQALLPPFFGTLKKYVE 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+QIREVAPERA+E RPFRLAIIQLGTYDGTIYNA
Sbjct: 241 YLETARNPFGFIGGIDAHCFKEAYLREQIREVAPERADEKRPFRLAIIQLGTYDGTIYNA 300

Query: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELNENDPGIIVTQSVHKQQAGF 360
           RQVVD+IGHLCDYILFDSAWVGYEQFIPMM DCSPLLLEL   DPGIIVTQSVHKQQAGF
Sbjct: 301 RQVVDRIGHLCDYILFDSAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGF 360

Query: 361 SQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHASTSPFYPLFAALDVNAKMHEGKSGQRL 420
           SQTSQIHKKDKHIKGQ+RYCNHKRFNNAFM+HASTS FYPLFAALDVNAKMHEG SG+ L
Sbjct: 361 SQTSQIHKKDKHIKGQARYCNHKRFNNAFMMHASTSHFYPLFAALDVNAKMHEGASGRYL 420

Query: 421 WKECVRVGIEARKMLLETCQLIKPFVPDQIDGKPWQSYDTETMANDLRFFNFVPGEKWHA 480
           W+E V+ GIEARK+LL+ C+ IKPF+P  IDG+ WQ Y TE MA+DLRFF F PG+KWH+
Sbjct: 421 WREAVKAGIEARKLLLKKCKYIKPFIPSMIDGRQWQDYPTEQMADDLRFFEFEPGQKWHS 480

Query: 481 FEGYAESQYFVDPCKLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSIL 540
           FEGY + QYFVDPCK LLTTPGID  +G Y++FGIPATILAN+LREN I+PEKCDLNSIL
Sbjct: 481 FEGYEKGQYFVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSIL 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+RGN+ELV L++ EGRIAAEGALPY
Sbjct: 601 NLYVSHDVKQLQKEMFRHAHFPTKVMDPQEANLEFIRGNVELVPLSQIEGRIAAEGALPY 660

Query: 661 PPGVLCVVPGEIWGGAAQRYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYVMS 719
           PPGVLC+VPGEIWGGA QRYFLALEEGINLLPGF+PELQGVY++   DG  +A GYV++
Sbjct: 661 PPGVLCMVPGEIWGGAVQRYFLALEEGINLLPGFSPELQGVYLESTPDGKIQALGYVLN 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: 1649
Number of extensions: 59
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 199509 SO0314 (ornithine decarboxylase, inducible (NCBI ptt file))
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.24109.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 1430.1   0.1          0 1429.9   0.1    1.0  1  lcl|FitnessBrowser__MR1:199509  SO0314 ornithine decarboxylase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199509  SO0314 ornithine decarboxylase, inducible (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1429.9   0.1         0         0       1     719 []       1     719 [.       1     719 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1429.9 bits;  conditional E-value: 0
                       TIGR04301   1 mkklkiavsesvkdafeterevveleetdftdvaavvlsvedvkagvlekieetafeipvfvvveeeekvsaellkkvt 79 
                                     mk+lk+a+s sv+++f+++revv++ +tdf+dv+a+v+sv+dvk g++eki++t++++p+fv v++ee++++++++++t
  lcl|FitnessBrowser__MR1:199509   1 MKSLKVAASLSVRSCFDIDREVVNVLTTDFCDVGAAVVSVDDVKDGIVEKIKNTGLKLPIFVSVCCEETFPDDICSSIT 79 
                                     99***************************************************************************** PP

                       TIGR04301  80 gvidleekdaelygrqleeaakkyeekllppffkalkkyvekgnsafdcpghqggeffrkhpagrqfvdffgenlfrsd 158
                                     gv++l+ +++++yg+q+e+a+kkye++llppff++lkkyve+gns+f+cpghqgg+ffrkhp+grqf+dffge++frsd
  lcl|FitnessBrowser__MR1:199509  80 GVFELCGSNTDFYGKQVETAIKKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETIFRSD 158
                                     ******************************************************************************* PP

                       TIGR04301 159 lcnadvalgdllihegaplaaqkhaakvfnadktyfvlngtsasnkvvlnallapgdlvlfdrnnhksnhhgallqaga 237
                                     +cnadv+lgdllihegapl+aqk+aakvfnadktyfvlngts+snkv++nalla+gdlvlfdrnnhksnhhgal+qaga
  lcl|FitnessBrowser__MR1:199509 159 MCNADVKLGDLLIHEGAPLDAQKYAAKVFNADKTYFVLNGTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGALIQAGA 237
                                     ******************************************************************************* PP

                       TIGR04301 238 tpvyletarnpfgfiggidehcfeeeylrelirevaperakekrpfrlaviqlgtydgtiynarqvvdkighlcdyilf 316
                                     tp+yletarnpfgfiggid+hcf+e+ylre+irevapera+ekrpfrla+iqlgtydgtiynarqvvd+ighlcdyilf
  lcl|FitnessBrowser__MR1:199509 238 TPIYLETARNPFGFIGGIDAHCFKEAYLREQIREVAPERADEKRPFRLAIIQLGTYDGTIYNARQVVDRIGHLCDYILF 316
                                     ******************************************************************************* PP

                       TIGR04301 317 dsawvgyeqfipmmkdcsplllelneedpgilvtqsvhkqqagfsqtsqihkkdkhikgqaryvnhkrlnnafmlhast 395
                                     dsawvgyeqfipmm+dcsplllel++edpgi+vtqsvhkqqagfsqtsqihkkdkhikgqary+nhkr+nnafm+hast
  lcl|FitnessBrowser__MR1:199509 317 DSAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQARYCNHKRFNNAFMMHAST 395
                                     ******************************************************************************* PP

                       TIGR04301 396 spfyplfaaldvnaklhegeagkrlwadcvktgiearklllkscklikpfvpelvdgkkwedydteeiandlrffefep 474
                                     s fyplfaaldvnak+heg++g+ lw+++vk+giearklllk+ck+ikpf+p+++dg++w+dy+te++a+dlrffefep
  lcl|FitnessBrowser__MR1:199509 396 SHFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCKYIKPFIPSMIDGRQWQDYPTEQMADDLRFFEFEP 474
                                     ******************************************************************************* PP

                       TIGR04301 475 gekwhsfegyeeeqyfvdpcklllttpgidvetgeyeefgvpatilanflrengiipekcdlnsilflltpaedlaklq 553
                                     g+kwhsfegye+ qyfvdpck+llttpgid+etg+y+efg+patilanflren+iipekcdlnsilfl+tpaed+ak+q
  lcl|FitnessBrowser__MR1:199509 475 GQKWHSFEGYEKGQYFVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDMAKMQ 553
                                     ******************************************************************************* PP

                       TIGR04301 554 elvaqiarfeklleedaplkevlpsvykaneerykgytirqlcqemhdlykernvkqlqkelfrkeylpkvvlnpqean 632
                                     +lv+qi+rfekl++edapl+evlp+vy+an++ryk+ytirqlcqemh+ly++++vkqlqke+fr++++p++v++pqean
  lcl|FitnessBrowser__MR1:199509 554 HLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVKQLQKEMFRHAHFPTKVMDPQEAN 632
                                     ******************************************************************************* PP

                       TIGR04301 633 leflrgevelveleeaegriaaegalpyppgvlcvvpgevwggavlkyflaleeginllpgfapelqgvyleededgrk 711
                                     lef+rg+velv+l+++egriaaegalpyppgvlc+vpge+wggav++yflaleeginllpgf+pelqgvyle++ dg+ 
  lcl|FitnessBrowser__MR1:199509 633 LEFIRGNVELVPLSQIEGRIAAEGALPYPPGVLCMVPGEIWGGAVQRYFLALEEGINLLPGFSPELQGVYLESTPDGKI 711
                                     ******************************************************************************* PP

                       TIGR04301 712 raygyvlk 719
                                     +a gyvl+
  lcl|FitnessBrowser__MR1:199509 712 QALGYVLN 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 10.17
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources