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_06130 H281DRAFT_06130 indolepyruvate ferredoxin oxidoreductase

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_06130 H281DRAFT_06130
            indolepyruvate ferredoxin oxidoreductase
          Length = 1176

 Score =  981 bits (2535), Expect = 0.0
 Identities = 546/1178 (46%), Positives = 735/1178 (62%), Gaps = 37/1178 (3%)

Query: 5    TPQLD-----DYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRG 59
            TP+++     DY+LEDRYLRE G VFLTGTQALVRI   QA  DR+ G+ +AGLVSGYRG
Sbjct: 5    TPEVERAIDHDYRLEDRYLREEGTVFLTGTQALVRILFEQARSDRRLGIKSAGLVSGYRG 64

Query: 60   SPLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYG 119
            SPLG  DQ LW+ K LL +  I F P +NEDL AT++ G QQ++    ++V+GVF +WYG
Sbjct: 65   SPLGGFDQELWRRKKLLKDADIRFEPGLNEDLGATMVWGAQQIDAFPGKRVDGVFAMWYG 124

Query: 120  KGPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPA 179
            KGPGVDR GD  ++    G+S  GGVL VAGDDH   SS  PHQ+D  F    MP I PA
Sbjct: 125  KGPGVDRTGDVFRNANILGTSARGGVLAVAGDDHAAQSSMFPHQTDHVFEGAMMPIIFPA 184

Query: 180  NIAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPA----PDFVTPDDFTAPE 235
            ++ EY++FGL GYA+SR+SG WV +KAI+ETVES  S+ +  +      F+TP D   P 
Sbjct: 185  SVEEYVKFGLAGYAMSRFSGLWVAYKAITETVESGRSMVVGRSDRANAGFLTPSDVEVPA 244

Query: 236  S-GLHYRWPDLPGP----QLETR-IEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGK 289
              G +Y  P LP P    +LE R IE +L A  AFARAN  D  L   ++AR GIVT GK
Sbjct: 245  GRGFNYD-PKLPWPSERTELERRIIEERLPAALAFARANPFDNTLVRPRDARVGIVTVGK 303

Query: 290  GHLDLLEALDLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGII 349
             H D+L AL  LG+D  +   +G+ +YKVGM WPLE  G+ +F  G   ++V+EEKR  +
Sbjct: 304  AHGDVLSALAKLGLDAAEMERLGIGLYKVGMTWPLETAGVHNFARGMSALMVVEEKRSFV 363

Query: 350  ESQIKEYMSEPDRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLG-RFFEVDF- 407
            E QIKE +          + GK+      L+P   ELSP  VA  L   L      VD  
Sbjct: 364  ERQIKESLFNVKASERPDVFGKELGDNSSLVPATLELSPGQVADSLRKFLAYTNVAVDVP 423

Query: 408  ------SERMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMAS 461
                  S        +T  +D   + R P+FC+GCPHNTSTK+P+GS A AGIGCH MA 
Sbjct: 424  TPAPIASSGRKSFPILTDGED-SVLTRKPFFCAGCPHNTSTKLPDGSYAAAGIGCHIMAL 482

Query: 462  WMGRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITY 521
                +T +  QMGGEG+ W+G S +T  PH+F NLG+GTY HSGS+AIRQAVAA  N+TY
Sbjct: 483  GDAGSTATFCQMGGEGIQWVGLSTFTEMPHMFINLGDGTYQHSGSLAIRQAVAAKANVTY 542

Query: 522  KILFNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTF 581
            KILFNDAVAMTGGQP +G +TV R+ +Q+ AEGV  V +++D+  KY       P +   
Sbjct: 543  KILFNDAVAMTGGQPTEGGLTVRRVVEQVQAEGVASVTIVTDDTSKYAA---TAPGNAAV 599

Query: 582  HDRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGD 641
              R ELD +QR+LR   G +V++Y+QTCAAEKRRRRKR        R  IN  VCEGCGD
Sbjct: 600  VHRDELDSLQRDLRKKKGVSVIVYEQTCAAEKRRRRKRGTMRTAPARVVINPAVCEGCGD 659

Query: 642  CSVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGS 701
            CSVQSNC+++ P  TE+GRKR ++QS+CNKD SCV GFCPSFVT+EG + RK     T +
Sbjct: 660  CSVQSNCIAIEPLDTEVGRKRAVNQSTCNKDTSCVKGFCPSFVTVEGLEPRKPDQARTEA 719

Query: 702  V---LTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFM 758
            V   L ++L + P P  PE+     ++V G+GGTGVVT+G +++MAAHLE RGAS LDF 
Sbjct: 720  VENELRQQLGN-PLPVPPEIRQHARIVVTGIGGTGVVTIGAILSMAAHLEGRGASTLDFT 778

Query: 759  GFAQKGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIV 818
            G AQK G VLS+V++A S  ++   RI    A+ +I CD VVASS+ ALS L  N T+ V
Sbjct: 779  GLAQKNGAVLSHVQIASSRGEISTSRIERQSANVLIGCDAVVASSKDALSRLVFNSTQTV 838

Query: 819  ANEAELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMM 878
             N    PT+D+V   D  +        +  AVG+      + N  AE + GD++  N+MM
Sbjct: 839  INTHITPTSDFVKNGDLALSESAHRKSIVAAVGDATSIFWNCNAAAETIFGDSIACNMMM 898

Query: 879  LGFAWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVV 938
            +GFA+Q+G++PLSEAA+M+AIELNG A+  NK AF WGRL A D  A+  L +      V
Sbjct: 899  VGFAFQRGMIPLSEAAIMRAIELNGAAVSMNKRAFLWGRLIAHDGCAIDRLTETP----V 954

Query: 939  EVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQL 998
             V+ +  LD+ + +R   L +YQN  +A +Y+  V  V   E  +      LT + A+  
Sbjct: 955  CVEEQFDLDQFVRSRMDDLTSYQNAAYAQRYKMLVDHVSAVERRVRGAVGDLTASAARSY 1014

Query: 999  YRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFG 1058
            ++ +AYKDEYEVARL ++  F K + ETFEG+ K  +H+APP++S      GR  K   G
Sbjct: 1015 FKVLAYKDEYEVARLHSDGSFSKRLAETFEGEGKFTYHMAPPVISRVDSRTGRRNKVALG 1074

Query: 1059 PWMFR-AFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETF 1117
             W  +   R+L   + LRG+ +DPF   +DR+L+RA++++++  V+     L+ +N++  
Sbjct: 1075 GWWLKPMLRVLKHGKLLRGSVLDPFSRQSDRRLERALIREFEDDVELALAHLSLTNHKAA 1134

Query: 1118 LQLAELPADVRGYGPVREQAAESIREKQTQLIKALDTG 1155
            L L  LP  +RG+G V+E + ++ ++++      L  G
Sbjct: 1135 LDLITLPLAIRGFGVVKENSYKAAQQRRCAYRTELSNG 1172


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: 2965
Number of extensions: 128
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: 1176
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1129
Effective search space:  1270125
Effective search space used:  1270125
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