Alignments for a candidate for iorAB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Pseudomonas fluorescens GW456-L13

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate PfGW456L13_3456 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3456
          Length = 1187

 Score = 1087 bits (2811), Expect = 0.0
 Identities = 563/1166 (48%), Positives = 765/1166 (65%), Gaps = 28/1166 (2%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L+D+Y++ SG+V LTG QALVR+PLMQ   D   GLNTAG +SGYRGSPLG  DQALW+A
Sbjct: 7    LDDKYIQHSGKVLLTGIQALVRLPLMQRQRDLANGLNTAGFISGYRGSPLGGFDQALWKA 66

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            +D L E+   F P +NEDLAAT + GTQQV   E    +GVFG+WYGKGPGVDR GD  +
Sbjct: 67   RDYLKEHHTVFHPGMNEDLAATSIWGTQQVNIFEGATYDGVFGMWYGKGPGVDRCGDVFR 126

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            H    G+S  GGVL +AGDDHG  SSS+PHQ++  F +  MP + P+ + EYL++G+ G+
Sbjct: 127  HANAAGTSQFGGVLAIAGDDHGARSSSLPHQTEHIFKAVMMPVLAPSGVQEYLDYGMHGW 186

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHYRWPDLPGPQLET 252
            A+SRYSGCWV  KA+++TVESAA V+I          D   PE GL+ RWPD P  Q + 
Sbjct: 187  AMSRYSGCWVALKAVADTVESAAVVDIDIHRVQPIIPDIPLPEGGLNIRWPDPPLAQEQR 246

Query: 253  RIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDMG 312
             +EHKL A  A+AR NR+DR + D+ +AR GI+T+GK +LD+ +AL +LGIDE  A+ +G
Sbjct: 247  LLEHKLYAALAYARVNRLDRIVMDSPKARIGIITSGKSYLDVCQALKILGIDETLAQQIG 306

Query: 313  LDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEVLITGKQ 372
            L +YKVGMVWPLE  G+  F  G EE++V+EEKR +IE Q+KE +          I GK 
Sbjct: 307  LRVYKVGMVWPLEAEGVRQFAEGLEEIVVVEEKRHMIEYQLKEELYNWREDVRPRIVGKF 366

Query: 373  DELGRPLIPYVG-------ELSPKLVAGFLAARLGRFFE---VDFSERMAEISAMTTAQD 422
            D+ G   +P+ G       +L+P ++A  LA R+    +   +  S  + +    +  Q 
Sbjct: 367  DDKGEWSLPHTGWLLPATNDLTPAMIARALAKRILHLHQNGPLQVSLAVLDAQLASKGQF 426

Query: 423  PGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWIG 482
               ++R+P++CSGCPHNTSTKVP+GS+ALAGIGCH+MA+W+   T++  QMGGEGV WIG
Sbjct: 427  SNLMERVPHYCSGCPHNTSTKVPQGSRALAGIGCHYMAAWIYPQTQTFSQMGGEGVAWIG 486

Query: 483  KSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQIT 542
            ++ +T   HVF NLG+GTYFHSG +AIR A+AA + ITYKIL+NDAVAMTGGQPVDG ++
Sbjct: 487  QAPFTKTRHVFANLGDGTYFHSGILAIRAAIAAKVQITYKILYNDAVAMTGGQPVDGSLS 546

Query: 543  VDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTV 602
            V +I++Q+AAEGV R+VV+SD+ EKY    DL    V    R ++D+VQ +LR   G + 
Sbjct: 547  VAQISRQLAAEGVQRIVVVSDDVEKYQHIRDL-ADGVPVLRRDKMDEVQEQLRQFQGVSA 605

Query: 603  LIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKR 662
            +IYDQTCAAEKRRRRKR +FPDPA+R  IN  VCEGCGDCS +SNC+SVV  +TE GRKR
Sbjct: 606  IIYDQTCAAEKRRRRKRGKFPDPARRVVINEAVCEGCGDCSSKSNCMSVVAVETEYGRKR 665

Query: 663  KIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSY 722
            +IDQSSCNKDF+C+NGFCPSFVT+EGG LRK + + +       + D+P P    +   Y
Sbjct: 666  EIDQSSCNKDFTCLNGFCPSFVTVEGGTLRKPKALASAK---NDVWDLPTPATVALEEPY 722

Query: 723  DLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQ 782
             +LV GVGGTGVVT+G L+ MAA +E +G   LD  G AQKGG V S++R+A   ++L  
Sbjct: 723  SILVTGVGGTGVVTIGALLGMAAFIEGKGTLNLDMAGMAQKGGAVWSHIRIAAHQEQLFA 782

Query: 783  VRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAE-------------LPTADY 829
             RI+ G+   ++ CDLVV+++ + LS LR   T  + N  E               T D 
Sbjct: 783  PRIAEGETALLLGCDLVVSANTETLSKLRHGVTHALINSEETITSAFVRTFAQQAETGDL 842

Query: 830  VLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLP 889
            +   D   +       +  AVG +H D +DA+ IA  LMGD++ +N  MLG+A+QKG LP
Sbjct: 843  LKHPDPTFQTGNMSEQIAEAVGTEHADFIDASKIATALMGDSIATNTFMLGYAYQKGWLP 902

Query: 890  LSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDEL 949
            + +AAL++AIELNG A+  N  AF WGR SA D   V   L+    Q  +     +L+E 
Sbjct: 903  VGKAALLQAIELNGTAVPFNLSAFDWGRRSAHDLPRVLRKLEAGKVQSPDRLLSQSLEET 962

Query: 950  INTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYE 1009
            +  R + L  YQN  +A +YR  V    KAE +L      L+ +VA+  ++ +A KDEYE
Sbjct: 963  LARRMEFLTAYQNYAYAQRYRYRVEQFIKAETALLGQPGKLSASVARYYFKVLAIKDEYE 1022

Query: 1010 VARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLA 1069
            VARLF +  F++++   FEGD+++ FHLAPPLL+ +  +   PKKR FGPWM + F+LLA
Sbjct: 1023 VARLFTDGQFLEKIQAGFEGDYRLRFHLAPPLLN-DNGSGREPKKRSFGPWMLQGFKLLA 1081

Query: 1070 KLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRG 1129
            +L+ LR T +DPF  + +RK++R  L +Y+ ++D +   L          L ELP  VRG
Sbjct: 1082 RLKFLRNTWLDPFGRTHERKVERNWLANYEQILDEVLAGLTTQKLGLAQDLVELPESVRG 1141

Query: 1130 YGPVREQAAESIREKQTQLIKALDTG 1155
            YGPV+E+     +++Q QL++    G
Sbjct: 1142 YGPVKERFLGHAQQRQAQLLEQWRNG 1167


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: 3030
Number of extensions: 152
Number of successful extensions: 9
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: 1187
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1140
Effective search space:  1282500
Effective search space used:  1282500
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.

Downloads

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