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_06130 H281DRAFT_06130 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Burk376:H281DRAFT_06130
          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 (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