Aligments for a candidate for odc in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for odc in Shewanella amazonensis SB2B

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 6939240 Sama_3334 ornithine decarboxylase (RefSeq)

Query= BRENDA::A4Q8H0
         (720 letters)



>lcl|FitnessBrowser__SB2B:6939240 Sama_3334 ornithine decarboxylase
           (RefSeq)
          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.16786.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: 00:00:00.06
# Mc/sec: 7.77
//
[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, 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

GapMind for catabolism of small carbon sources