Alignments for a candidate for iorAB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Marinobacter adhaerens HP15

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate GFF880 HP15_859 pyruvate ferredoxin/flavodoxin oxidoreductase

Query= reanno::Marino:GFF880
         (1172 letters)



>FitnessBrowser__Marino:GFF880
          Length = 1172

 Score = 2355 bits (6102), Expect = 0.0
 Identities = 1172/1172 (100%), Positives = 1172/1172 (100%)

Query: 1    MSADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGS 60
            MSADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGS
Sbjct: 1    MSADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGS 60

Query: 61   PLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGK 120
            PLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGK
Sbjct: 61   PLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGK 120

Query: 121  GPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPAN 180
            GPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPAN
Sbjct: 121  GPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPAN 180

Query: 181  IAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHY 240
            IAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHY
Sbjct: 181  IAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHY 240

Query: 241  RWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDL 300
            RWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDL
Sbjct: 241  RWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDL 300

Query: 301  LGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEP 360
            LGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEP
Sbjct: 301  LGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEP 360

Query: 361  DRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVDFSERMAEISAMTTA 420
            DRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVDFSERMAEISAMTTA
Sbjct: 361  DRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVDFSERMAEISAMTTA 420

Query: 421  QDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNW 480
            QDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNW
Sbjct: 421  QDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNW 480

Query: 481  IGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQ 540
            IGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQ
Sbjct: 481  IGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQ 540

Query: 541  ITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGC 600
            ITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGC
Sbjct: 541  ITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGC 600

Query: 601  TVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGR 660
            TVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGR
Sbjct: 601  TVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGR 660

Query: 661  KRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTG 720
            KRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTG
Sbjct: 661  KRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTG 720

Query: 721  SYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKL 780
            SYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKL
Sbjct: 721  SYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKL 780

Query: 781  HQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKAD 840
            HQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKAD
Sbjct: 781  HQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKAD 840

Query: 841  KRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIE 900
            KRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIE
Sbjct: 841  KRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIE 900

Query: 901  LNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNY 960
            LNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNY
Sbjct: 901  LNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNY 960

Query: 961  QNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFM 1020
            QNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFM
Sbjct: 961  QNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFM 1020

Query: 1021 KEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAID 1080
            KEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAID
Sbjct: 1021 KEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAID 1080

Query: 1081 PFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAES 1140
            PFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAES
Sbjct: 1081 PFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAES 1140

Query: 1141 IREKQTQLIKALDTGRPTLIRTQQANEEANHV 1172
            IREKQTQLIKALDTGRPTLIRTQQANEEANHV
Sbjct: 1141 IREKQTQLIKALDTGRPTLIRTQQANEEANHV 1172


Lambda     K      H
   0.319    0.136    0.405 

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: 3857
Number of extensions: 126
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: 1172
Length of database: 1172
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1125
Effective search space:  1265625
Effective search space used:  1265625
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 (21.7 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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