GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_01671
          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 (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:

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. 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:

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:

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