GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iorAB in Dechlorosoma suillum PS

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate Dsui_0379 Dsui_0379 indolepyruvate ferredoxin oxidreductase, alpha/beta subunit

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



>lcl|FitnessBrowser__PS:Dsui_0379 Dsui_0379 indolepyruvate ferredoxin
            oxidreductase, alpha/beta subunit
          Length = 1183

 Score = 1128 bits (2918), Expect = 0.0
 Identities = 587/1174 (50%), Positives = 788/1174 (67%), Gaps = 32/1174 (2%)

Query: 7    QLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVD 66
            +L    L+D+Y   SGR FLTGTQAL+R+P++Q   D+ QGLNTAG +SGYRGSPLG +D
Sbjct: 11   ELASASLDDKYTTLSGRAFLTGTQALIRLPMLQRLRDQAQGLNTAGFISGYRGSPLGGLD 70

Query: 67   QALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDR 126
            Q LW+A+  L EN I F P +NEDLAAT + G+QQV      + +GVF LWYGKGPGVDR
Sbjct: 71   QGLWKAQKYLAENHITFQPGVNEDLAATAVWGSQQVNLFPGAKYDGVFALWYGKGPGVDR 130

Query: 127  AGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLE 186
            +GD  +H    GSS HGGVLVVAGDDH   SS++PHQ++  F +  MP + PAN+ EYLE
Sbjct: 131  SGDVFRHANAAGSSRHGGVLVVAGDDHAAKSSTLPHQTEHVFKAVMMPVLYPANVQEYLE 190

Query: 187  FGLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDL 245
            +GL G+A+SRYSGCWV FKA+++TVE++ASV + P A D   PDDF  P  GL+ RWPD 
Sbjct: 191  YGLHGWAMSRYSGCWVAFKALADTVETSASVWVDPMALDIRLPDDFELPADGLNIRWPDP 250

Query: 246  PGPQLETRIEH-KLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGID 304
            P  Q E R+ H KL A  A+ARANR++R + D+   R GI+T GK +LD+++ALD LGID
Sbjct: 251  PLVQ-EARLTHFKLYAALAYARANRLNRIVIDSPAPRLGIITAGKSYLDVMQALDELGID 309

Query: 305  EDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPG 364
            +  A  +G+ +YKVGMVWPLE  G+  F  G +E+LV+EEKR ++E Q+KE +       
Sbjct: 310  QQLAAQIGIRLYKVGMVWPLESEGVRQFAEGLDEILVVEEKRQMLEYQLKEELYNWREDV 369

Query: 365  EVLITGKQDELGR---------------PLIPYVGELSPKLVAGFLAARLGRFF-EVDFS 408
               + GK DE G                 L+P  GELS   +A  +A+R+ R F      
Sbjct: 370  RPRVVGKFDEKGEWALLPDGKGHLAHGDWLLPAAGELSVAQIARAIASRIERHFTSPAIK 429

Query: 409  ERMAEISAMTTAQDPGGV--KRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRN 466
             R+  I A   A     +  +R P+FCSGCPHNTST+VPEGS+A+AGIGCH+M +WM R+
Sbjct: 430  ARLDLIEAKQKALQTPLILTQRTPHFCSGCPHNTSTRVPEGSRAVAGIGCHYMVTWMDRS 489

Query: 467  TESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFN 526
            T +   MGGEGV W+G++ +T   H+F NLG+GTYFHSG +AIRQ+VAA  NITYKIL+N
Sbjct: 490  TSTFTHMGGEGVTWVGQAPFTEEKHIFANLGDGTYFHSGLLAIRQSVAAKTNITYKILYN 549

Query: 527  DAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSE 586
            DAVAMTGGQPVDG ++V RI +Q+ AEGV R+V+++DEPEKY    DL P +V    R E
Sbjct: 550  DAVAMTGGQPVDGILSVPRITRQLEAEGVGRMVIVTDEPEKYAEVTDLAP-NVPVRHRDE 608

Query: 587  LDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQS 646
            LD VQRELR+IPG T+LIYDQTCA EKRRRRKR +  D  +R FIN  VCEGCGDCSVQS
Sbjct: 609  LDAVQRELREIPGTTILIYDQTCATEKRRRRKRGKLADVDRRVFINEAVCEGCGDCSVQS 668

Query: 647  NCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRK 706
            NCLSV+P +T+ GRKR IDQS+CNKDFSC+ GFCPSFVT+EG +L+K + +   ++  + 
Sbjct: 669  NCLSVIPVETDFGRKRAIDQSNCNKDFSCLKGFCPSFVTLEGAKLKKGQAL---AMDAQD 725

Query: 707  LADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGT 766
               +P P LP     Y+LLV GVGGTGVVT+G LI MAAHL+ +G SVLD  G AQK G 
Sbjct: 726  WPPLPEPVLPPTARPYNLLVTGVGGTGVVTLGALIGMAAHLDGKGVSVLDMTGLAQKYGA 785

Query: 767  VLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPT 826
            V +++R A  P+ +H  RI+ G+ADA++  D+VV +  +ALS +    TR V N  E PT
Sbjct: 786  VFTHLRFADRPEDIHAARIATGEADAILGGDVVVTAGNEALSKMLEGRTRAVVNCTETPT 845

Query: 827  ADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKG 886
            A++    D      +    +   VG DH   LDA  +A  LMGD +++N+ +LG+AWQKG
Sbjct: 846  AEFTRNPDWQFPLARMQQTVTATVGADHAWFLDAQALATALMGDALYTNMFLLGYAWQKG 905

Query: 887  LLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTL 946
            L+P+S  AL +AIELNG A+  N +A  WGR +AVD + V  L   + A     +P+  L
Sbjct: 906  LVPVSLPALGRAIELNGTAVAANLQALDWGRRAAVDEARVRQLATPA-ADTPPPRPDAAL 964

Query: 947  DELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKD 1006
            +E++  R + L +YQ+   A +YR  +  +R+AE  L +  L +T A A+  ++ +A KD
Sbjct: 965  EEVLALREQELTDYQDAALARRYRQRIEALRQAEAPL-DPALPVTLAAARNYFKVLAIKD 1023

Query: 1007 EYEVARLFAETDFMKEVNETFEG----DFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMF 1062
            EYEVARL    +F   + +TF G    D+ VH HLAPPL +      G+ +KR++GPWM 
Sbjct: 1024 EYEVARLHTRPEFFARLRQTFAGEPGKDYAVHVHLAPPLWARPDPRSGQIRKRQYGPWML 1083

Query: 1063 RAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNA-SNYETFLQLA 1121
             A +LLA+L+ LRGTA+D F ++A+R+++RA+   Y++ ++RI   L A S +   L+LA
Sbjct: 1084 GALKLLARLKFLRGTALDVFGHTAERRMERALQAGYEADLERILEALAAGSAHPALLELA 1143

Query: 1122 ELPADVRGYGPVREQAAESIREKQTQLIKALDTG 1155
             LP  VRGYG V+  +AE  R+++ +L++ L+ G
Sbjct: 1144 RLPESVRGYGHVKAASAEKARQQRQELLRKLEGG 1177


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: 3147
Number of extensions: 130
Number of successful extensions: 10
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: 1183
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1136
Effective search space:  1278000
Effective search space used:  1278000
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, the preprint on GapMind for carbon sources, 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