GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_0379
          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 (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