GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iorAB in Paraburkholderia bryophila 376MFSha3.1

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate H281DRAFT_01671 H281DRAFT_01671 indolepyruvate ferredoxin oxidoreductase

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_01671 H281DRAFT_01671
            indolepyruvate ferredoxin oxidoreductase
          Length = 1184

 Score = 1063 bits (2749), Expect = 0.0
 Identities = 555/1171 (47%), Positives = 768/1171 (65%), Gaps = 22/1171 (1%)

Query: 1    MSADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGS 60
            +  +T    +  L+D+Y +E G  +++G+ AL+R+ + Q   D   GLNTAG VSGYRGS
Sbjct: 6    IEVETAPTSEVSLDDKYRKERGYAYMSGSHALIRVMINQRIRDNDAGLNTAGFVSGYRGS 65

Query: 61   PLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVET-DEDRQVEGVFGLWYG 119
            PL   D ALW A+ +L +++I F+PAINEDLAAT + GTQQ+    ++  VEGVF +WYG
Sbjct: 66   PLAGFDTALWSAEAVLKQHQIKFLPAINEDLAATAVWGTQQLALFPQESTVEGVFSMWYG 125

Query: 120  KGPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPA 179
            KGPGVDR+GDALKHG   G+S  GGVLV A DDH   SS+  HQS+ A ++ F+P + PA
Sbjct: 126  KGPGVDRSGDALKHGNGAGTSALGGVLVAAADDHTAKSSTFGHQSEQALIAAFIPVLYPA 185

Query: 180  NIAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAP-DFVTPDDFTAPESGL 238
            ++ +YL+FG+ G A+ RYSG W+G K +S+ +E++A  ++ P   D   PD   A +  L
Sbjct: 186  SVQDYLDFGVLGIAMGRYSGLWIGLKCVSDVIETSAVADVDPHRIDIRLPDKEFAADDDL 245

Query: 239  HYRWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEAL 298
            H R PD+   Q    +  +L A  AF RANR++       +++ GI+  GK + D++EAL
Sbjct: 246  HIRSPDVWAEQEPRIVRKRLPAALAFCRANRLNSIRIKGPKSKLGIMCAGKAYNDVMEAL 305

Query: 299  DLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMS 358
             LLG+ +D     GL + K+GMVWPL+   + DF  G +E+LV+EEKR IIE QIK+ + 
Sbjct: 306  RLLGLSDDDIEKNGLAVLKIGMVWPLDPTILRDFAAGLDELLVVEEKRPIIEQQIKDELY 365

Query: 359  EPDRPGEVLIT----------GKQDELGRP-LIPYVGELSPKLVAGFLAARLG------R 401
                 G  L+           G+ +  G   L+    EL+P  VAG + ARL        
Sbjct: 366  SDALNGLPLVRVSGKGSGAIGGEWNRSGEACLLRSDYELTPVEVAGAIVARLRAQAGWTE 425

Query: 402  FFEVDFSERMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMAS 461
              + +   R+A + A+   Q   G  R P+FCSGCPHNTST+VPEGS+A AGIGCH+MAS
Sbjct: 426  TRKREIEARLAALEAVGRVQAVAGAIRKPFFCSGCPHNTSTRVPEGSRATAGIGCHYMAS 485

Query: 462  WMGRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITY 521
             M R TES   MGGEGV W+ +++++   H+F N+G+GTYFHSGS+AIRQAVAA +++T+
Sbjct: 486  SMDRRTESYTHMGGEGVPWVAQAQFSTRKHIFANIGDGTYFHSGSLAIRQAVAARVSMTF 545

Query: 522  KILFNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTF 581
            KIL+NDA AMTGGQPVDG++TVD I +Q+AAEGV R+ V+SD+ E+Y      F    T 
Sbjct: 546  KILYNDAAAMTGGQPVDGELTVDGITRQVAAEGVRRIAVVSDDIEQYRISGTTFAAGTTV 605

Query: 582  HDRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGD 641
            HDRSELD VQR LRD  G +VL+YDQTCA+EKRRRRK+  +PDPAKR  IN  VCEGCGD
Sbjct: 606  HDRSELDAVQRNLRDYEGVSVLVYDQTCASEKRRRRKKGTYPDPAKRVAINSEVCEGCGD 665

Query: 642  CSVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGS 701
            CSVQSNCLSV P  T LGRKR+I+QSSCNKDFSCV GFCPSFV++EGG+LR S+   +  
Sbjct: 666  CSVQSNCLSVEPLDTPLGRKRQINQSSCNKDFSCVQGFCPSFVSVEGGKLRSSQTKKSPE 725

Query: 702  VLTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFA 761
             +     ++P P  P MT + D+L+ GVGGTGVVT+G L+ MAAHLE RG +VLD  G A
Sbjct: 726  AMMADWPELPYPASPAMTDTVDILINGVGGTGVVTIGNLLGMAAHLEGRGCTVLDMAGLA 785

Query: 762  QKGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANE 821
            QKGG V S+VR+A   ++++  RI +G AD +I CDLVV ++   LS +R   TR+V N 
Sbjct: 786  QKGGAVWSHVRLASKRERMYASRIPSGSADVIIGCDLVVTAAPDTLSRIRKGKTRVVING 845

Query: 822  AELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGF 881
               PT+ +V  RD  +   +    +++  G+D  D +DA  IA + +GDTVFSN +MLGF
Sbjct: 846  QTSPTSAFVANRDWQLPEAELKSHVESVCGDDFVDWVDAQEIARRHLGDTVFSNAIMLGF 905

Query: 882  AWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVK 941
             WQ+GL+PL+  ++ +AIELNG A+ +NK AF  GR  AV+P+      +  +  V   K
Sbjct: 906  VWQQGLIPLARESIERAIELNGQAVKKNKLAFQIGRWLAVNPARFAAGEEVESVIVWRQK 965

Query: 942  PEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRF 1001
             +  LDELI +R   L  YQ++R+A +Y   V+ +     S G+    +  AVA+ LY+ 
Sbjct: 966  KKVVLDELIQSRVSLLAAYQSERYAREYETFVSEITAQVGSHGKREAFIL-AVAEGLYKL 1024

Query: 1002 MAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWM 1061
            MAYKDEYEVARL++   F K +   FEGDFK+ ++LAPP+LS + + +G   K+ FGPW+
Sbjct: 1025 MAYKDEYEVARLYSLPGFKKSLENQFEGDFKIRYYLAPPMLSRKNE-KGELIKKEFGPWL 1083

Query: 1062 FRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLA 1121
               F LLA+L+ LRGT  DPF ++A+R+ +RA++++Y+  + R      A   +  ++LA
Sbjct: 1084 GHVFPLLARLKILRGTPFDPFGHTAERRRERALIREYRLWI-RTALTHLADKPDVCIELA 1142

Query: 1122 ELPADVRGYGPVREQAAESIREKQTQLIKAL 1152
            +LP  +RGYG V+E+A + +  K+  L+ AL
Sbjct: 1143 KLPDSIRGYGHVKERAIDEVMAKRDTLLAAL 1173


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: 2962
Number of extensions: 110
Number of successful extensions: 7
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: 1184
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1137
Effective search space:  1279125
Effective search space used:  1279125
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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, 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