Alignments for a candidate for iorAB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Phaeobacter inhibens BS107

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate GFF1685 PGA1_c17080 pyruvate ferredoxin/flavodoxin oxidoreductase-like protein

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



>FitnessBrowser__Phaeo:GFF1685
          Length = 1139

 Score =  966 bits (2497), Expect = 0.0
 Identities = 514/1154 (44%), Positives = 729/1154 (63%), Gaps = 42/1154 (3%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L D++     +V L GTQALVR+ LMQ   D+  GLNTAGLV+GYRGSPLGAVD  + +A
Sbjct: 8    LNDKFDLTKSQVMLNGTQALVRLMLMQKHRDKAAGLNTAGLVTGYRGSPLGAVDMQMKRA 67

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            +  L  + + F   +NEDLA T L G QQ E   + + +GVFGLWYGKGPGVDR+GDA++
Sbjct: 68   EKHLTASDVTFQFGLNEDLAVTALWGAQQAEVRGEGKYDGVFGLWYGKGPGVDRSGDAIR 127

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            H    GSS HGGVLV  GDDH   SS++ HQS+ + M  ++P ++PA + E L++G +G 
Sbjct: 128  HANMAGSSKHGGVLVAMGDDHTGESSTVLHQSEWSLMDCYLPIVSPAGVQEILDYGAYGL 187

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHYRWPDLPGPQLET 252
            ALSR+SG WVG K + +T+E  + V+  P    +   +F  P  GL+ R  D    Q   
Sbjct: 188  ALSRFSGLWVGLKTMKDTIEVTSVVDGDPDRMKLVTPEFDMPADGLNIRLDDDRFRQENR 247

Query: 253  RIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDMG 312
             I++K  A +AF+ AN++D+ ++    A+ G V  GK  LDL+ A+ LL IDE  A  +G
Sbjct: 248  IIDYKRFAAEAFSHANKMDKRMWGKPGAKIGFVAAGKNWLDLVHAMSLLNIDETMAERLG 307

Query: 313  LDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEVLITGKQ 372
            +  YKVG  WPL+ +G  D+  G + ++V+EEKR +IE QIKE + + DR G  +    +
Sbjct: 308  ITTYKVGQTWPLDMKGFNDWAEGLDLIVVVEEKRKLIEIQIKEAIFD-DRQGRRVYGWYK 366

Query: 373  DELG----RPLIPYVGELSPKLVAGFLAARLGRFFEVDFSERMAEISAMTTAQDPGG--- 425
               G      L P    L P ++    A +LG+    +  E  A  + +T   D      
Sbjct: 367  GGAGAMHREELFPTKYALDPIMI----AEKLGQILIEEGRETEAIRAGLTALDDAKRADN 422

Query: 426  ----VKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWI 481
                  R+PYFCSGCPHN+STK+P+GS+A AGIGCHFM  WM R T     MGGEGVNW+
Sbjct: 423  AEEIAARLPYFCSGCPHNSSTKLPDGSRAYAGIGCHFMVQWMDRETTGFTHMGGEGVNWV 482

Query: 482  GKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQI 541
            G++ ++   HVFQNLG+GTY HSG  AIR A+A G NIT+KIL+NDAVAMTGGQ  +G +
Sbjct: 483  GEAPFSNRKHVFQNLGDGTYNHSGVQAIRAALAEGTNITFKILYNDAVAMTGGQEAEGGL 542

Query: 542  TVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCT 601
            T  +IA ++ A G+  + V+ DE E  D    LFP  +  H+R+EL  VQ+E+  + G +
Sbjct: 543  TAHQIAHELTAMGMKTIAVVYDEKEDVDA--KLFPAGMRMHERAELMAVQKEMETVEGVS 600

Query: 602  VLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRK 661
             +IY QTCAAEKRRRRK+  FPDP +R FIN  VCEGCGDC VQSNC+S+VP++TELGRK
Sbjct: 601  AIIYIQTCAAEKRRRRKKGLFPDPDQRVFINSDVCEGCGDCGVQSNCVSIVPKETELGRK 660

Query: 662  RKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGS 721
            R IDQSSCNKDFSCV GFCPSF+TIEG ++RK             L D+P P+LP + G+
Sbjct: 661  RAIDQSSCNKDFSCVKGFCPSFLTIEGAKIRKE------PTAALDLPDLPKPELPSINGT 714

Query: 722  YDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLH 781
            +++++ GVGGTGVVT+G ++  AA ++ +GA +++  G AQKGG V  + R+A  P+ + 
Sbjct: 715  HNVVITGVGGTGVVTIGAVLAQAAQIDGKGAGMMEMAGLAQKGGAVHIHCRIANKPEDIS 774

Query: 782  QVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADK 841
             +R++ G+A A+I  DLVV++  K + +++   T  V N  E+ T D+    D  +  D 
Sbjct: 775  AIRVATGEAHALIGGDLVVSAGAKTIGLMKTGKTGAVVNSHEIITGDFTRDTDFQLPTD- 833

Query: 842  RLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIEL 901
            RL +   A   D  D  DA+ +A   MGD++FSN+M+ G AWQ+GLLP+S  A+ +AI L
Sbjct: 834  RLQVALEARLRDRLDLFDASDLARASMGDSIFSNMMIFGAAWQRGLLPISLEAIQEAITL 893

Query: 902  NGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNYQ 961
            NG A++RN  AF  GR + + P  V  L+  +   VVE+    +L+E I  R   LV+YQ
Sbjct: 894  NGAAVERNLRAFDIGRWAVLYPQEVQKLIAPN---VVEL--PKSLEEQIAFRSAQLVDYQ 948

Query: 962  NQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFMK 1021
              R A +Y   + G+  A+++L E       +VA+  ++ ++YKDEYEVARL   +   +
Sbjct: 949  GPRLAKRYGKMLDGI--ADKALKE-------SVAKGYHKLLSYKDEYEVARLLLSS--RE 997

Query: 1022 EVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAIDP 1081
            +    FEGD K+ ++LAPP+L+G+ D  GRPKKR+FGP + R  RLLAK +GLRGT +D 
Sbjct: 998  KAEAEFEGDLKISYNLAPPMLTGK-DPDGRPKKRKFGPGLERGLRLLAKFKGLRGTPLDV 1056

Query: 1082 FRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAESI 1141
            F Y+A+RK++RA++  Y++ +     + +       + LAELP ++RG+GPV++      
Sbjct: 1057 FGYTAERKMERALIAQYEADMKEWLPKASPEIMAPLIALAELPLEIRGFGPVKQANESKA 1116

Query: 1142 REKQTQLIKALDTG 1155
             +++ +L+ AL  G
Sbjct: 1117 AKRREELLAALRHG 1130


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: 3009
Number of extensions: 132
Number of successful extensions: 10
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: 1139
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1092
Effective search space:  1228500
Effective search space used:  1228500
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 Sep 17 2021. 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 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