Alignments for a candidate for iorAB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Pseudomonas stutzeri RCH2

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate GFF3452 Psest_3517 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

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



>FitnessBrowser__psRCH2:GFF3452
          Length = 1156

 Score = 1122 bits (2901), Expect = 0.0
 Identities = 561/1155 (48%), Positives = 785/1155 (67%), Gaps = 21/1155 (1%)

Query: 8    LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67
            L + +L+D+Y   +G ++LTGTQAL R+P++Q   D+ +GLNT G +SGYRGSPLG +D+
Sbjct: 3    LAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDK 62

Query: 68   ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127
            +LW+A+D L ++ I F P +NE+LAAT + G+QQ       + +GVF +WYGKGPGVDRA
Sbjct: 63   SLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRA 122

Query: 128  GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187
            GD  KH    G SP GGVL++AGDDHGC SS++PHQS+ AF++  +P +NPAN+ E L++
Sbjct: 123  GDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDY 182

Query: 188  GLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDLP 246
            G+ G+ LSRYSGCWV  K I+E V+S+A VE+ P       P+DF  PE G+H RWPD P
Sbjct: 183  GIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPP 242

Query: 247  GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306
              Q +    +K+ A +AFARAN ++R + D+   R GI+TTGK +LD+ +ALD LG+DE 
Sbjct: 243  LAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEA 302

Query: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366
                +GL + KVGM WPLE   + +F  G +E+LV+EEKR IIE Q+   +         
Sbjct: 303  LCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRP 362

Query: 367  LITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVD-FSERMAEISA--MTTAQDP 423
             + G+ DE G  L+P + EL+P ++A  +A RL   +  D    R+A ++A     A   
Sbjct: 363  RVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARS 422

Query: 424  GGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWIGK 483
                R P++CSGCPHN+STKVPEGS+A AGIGCH+M  WM R TE+  QMGGEGVNWIG+
Sbjct: 423  YSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQ 482

Query: 484  SRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQITV 543
            + +T  PH+FQNLG+GTYFHSGS+A+R AVAAG+N+TYKIL+NDAVAMTGGQP+DG++ V
Sbjct: 483  APFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRV 542

Query: 544  DRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTVL 603
            D++++Q+  EGV R+ ++SDEP+KY    D F    +FH R ELD VQRELR+  G +V+
Sbjct: 543  DQLSRQIFHEGVKRIALVSDEPDKYPS-RDTFAPITSFHHRRELDAVQRELREFKGVSVI 601

Query: 604  IYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKRK 663
            IYDQTCA EKRRRRKR +  DPAKRAFIN  VCEGCGDC  +SNCL+V+P +TELGRKR+
Sbjct: 602  IYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKRE 661

Query: 664  IDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSYD 723
            IDQ++CNKDFSCV GFCPSFVT+ GG LRK   V  G     + A +P P+ P +   ++
Sbjct: 662  IDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGI----EAATLPEPQHPTLDRPWN 717

Query: 724  LLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQV 783
            +L+ GVGG+GV T+G L+ MAAHLE +G +VLD  G AQK G V ++VR+A     ++ V
Sbjct: 718  VLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAV 777

Query: 784  RISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADKRL 843
            RI+ G+AD ++ CDL+VA+  ++L+ L    +  V N  E  TA++    DA +      
Sbjct: 778  RIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMR 837

Query: 844  GLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIELNG 903
              + +AVG D    +DA  +A +L+GD++ +N+ +LGFA+Q+GLLP+S  A+ KAIELNG
Sbjct: 838  QAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNG 897

Query: 904  VAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEP---TLDELINTRHKHLVNY 960
            V+   N +AF WGR + ++  AV  L     A+ V++  EP   TL+E+++ R   L  Y
Sbjct: 898  VSAKLNLQAFRWGRRAVLEREAVEQL-----ARPVDM-VEPICKTLEEIVDWRVDFLTRY 951

Query: 961  QNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFM 1020
            Q+   A +YR  V  VR A+ +    +L L++AVA+  ++ +AYKDEYEVARL++E +F 
Sbjct: 952  QSAGLARRYRQLVERVRDADSA---DDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFR 1008

Query: 1021 KEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAID 1080
            +++   FEGD+K+ FHLAP  L+      G P+KR  GPW+   F +LAK R LRGT +D
Sbjct: 1009 QQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLD 1068

Query: 1081 PFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAES 1140
            PF Y  DR+++R ++ +Y+  VD +  +L  +NY T + +A LP  +RGYGPV+E++   
Sbjct: 1069 PFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAK 1128

Query: 1141 IREKQTQLIKALDTG 1155
             R+++  L + L  G
Sbjct: 1129 ARQQEKLLREQLAKG 1143


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: 121
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1172
Length of database: 1156
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1109
Effective search space:  1247625
Effective search space used:  1247625
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