Alignments for a candidate for iorAB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Cupriavidus basilensis 4G11

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate RR42_RS10350 RR42_RS10350 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Cup4G11:RR42_RS10350
          Length = 1162

 Score =  993 bits (2566), Expect = 0.0
 Identities = 545/1168 (46%), Positives = 713/1168 (61%), Gaps = 36/1168 (3%)

Query: 9    DDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQA 68
            D Y+LEDRY RE+G VFLTGTQALVRI + QA  DR  GL T GLVSGYRGSPLG  DQ 
Sbjct: 3    DTYRLEDRYRREAGSVFLTGTQALVRILVEQARADRIAGLKTGGLVSGYRGSPLGGFDQE 62

Query: 69   LWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAG 128
            LW+ + LL E  I F P +NEDL AT+L G QQ++    ++VEGVF +WYGKGPGVDR G
Sbjct: 63   LWRQRSLLAEYEIRFEPGLNEDLGATMLWGAQQIDAFPGKRVEGVFSMWYGKGPGVDRTG 122

Query: 129  DALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFG 188
            D  ++    G+S HGGVL +AGDDH   SS  PHQ+D  F    MP + PA++ EY+EFG
Sbjct: 123  DVFRNANVLGTSRHGGVLAIAGDDHAAQSSMFPHQTDHVFEGAMMPVLFPASVEEYVEFG 182

Query: 189  LWGYALSRYSGCWVGFKAISETVESAASVEIPPAPD-----FVTPDDFTAPESGLHY--- 240
            L+GYALSR+SG WV FKAI+ETVES  S+ I  A       F  P D   PE G  Y   
Sbjct: 183  LFGYALSRFSGLWVAFKAITETVESGRSMLIGGAGSARGARFSLPGDIDIPERGFGYDTG 242

Query: 241  -RWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALD 299
             +WP          +E +L A QAFARAN IDR +   ++AR GIVT GK H DLL AL 
Sbjct: 243  VKWPGQRAELERRLLEERLPAAQAFARANPIDRTIVRPRDARIGIVTVGKAHGDLLAALA 302

Query: 300  LLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSE 359
             LG+DE +  ++G+ +YK+GM WP+E  G+  F  G   +LV+EEKR  +E QI+E +  
Sbjct: 303  RLGLDEPRLAELGIGLYKIGMTWPIEGEGVRRFASGMRALLVVEEKRSFVERQIQETLFN 362

Query: 360  PDRPGEVLITGKQDELGRPLIPYVGELSP----KLVAGFL------AARLGRFFEVDFSE 409
               P    + GK+     PL+P   E +P    K +  FL      A   G         
Sbjct: 363  VAAPQRPEVFGKRGPNDAPLLPATLEFAPDQLQKALRQFLAYTGVHALPPGNTGSAAALP 422

Query: 410  RMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTES 469
            R   +  ++    P  + R P+FC+GCPHN+STK+P+GS A AGIGCH MA   G NT +
Sbjct: 423  RQPRVIPLSAQLQPDVLTRKPFFCAGCPHNSSTKLPDGSYAAAGIGCHIMALGQGDNTAT 482

Query: 470  LIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAV 529
              QMGGEGV W+G S ++  PH+F NLG+GTY HSGS+AIRQAVAAG  +TYKILFNDAV
Sbjct: 483  FCQMGGEGVQWVGLSSFSDLPHLFVNLGDGTYQHSGSLAIRQAVAAGTAVTYKILFNDAV 542

Query: 530  AMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQ 589
            AMTGGQP +G +TV R+  Q+ AEGV +VV++SD P++Y G   + P  V    R  LD 
Sbjct: 543  AMTGGQPTEGGLTVPRMVAQLIAEGVGKVVLVSDHPQRYWGAKSI-PASVEIAHRDALDD 601

Query: 590  VQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCL 649
            VQR LR   G + ++YDQTCAAEKRRRRKR    DP +R  IN  VCEGCGDCSVQSNC+
Sbjct: 602  VQRRLRAYRGVSAIVYDQTCAAEKRRRRKRGTLADPVRRVVINPSVCEGCGDCSVQSNCI 661

Query: 650  SVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLAD 709
            ++ P +T LGRKR ++QSSCNKD SC+ GFCPSFVTIEG Q +++       +  +  A 
Sbjct: 662  AIEPLETPLGRKRAVNQSSCNKDMSCLKGFCPSFVTIEGLQPKRANQRRIQQMEAQWRAS 721

Query: 710  IPAPKLPEMTGSY----DLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGG 765
            +P P  P   G+      +LV GVGGTGVVTVG ++ MAAHLE +GA+ LDF G AQK G
Sbjct: 722  LPPPAGPAALGALLEHARILVTGVGGTGVVTVGAILAMAAHLEGKGAATLDFTGLAQKNG 781

Query: 766  TVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELP 825
             V+S+V++A   +++   RI    AD +I CD VVA+S   L+ LR   TR V N A  P
Sbjct: 782  AVVSHVQLADRRERIVTARIEACSADVMIGCDAVVAASPDVLARLRKCGTRAVVNSAVAP 841

Query: 826  TADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQK 885
            TAD+V   D  +  +     +++ VG    +  D    A  L GD + +N+M++G A+Q+
Sbjct: 842  TADFVANGDLPISREIHQAAIESVVGAGQAEFFDCTAAAMTLFGDAIATNMMLVGHAYQR 901

Query: 886  GLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAV--TDLLDDSNAQVVEVKPE 943
            G +PLSE A+ +AIELNG A++ N+ AF WGR+ A +P+A+  T   +   AQ  E    
Sbjct: 902  GWIPLSEMAIARAIELNGAAVELNRRAFLWGRILACEPNALRRTSAAEAQAAQPFE---- 957

Query: 944  PTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMA 1003
              L   +  R + L  YQN  +A++Y   VA V  AE+ +     LL  AVA+  YR +A
Sbjct: 958  --LARFVAERKRDLSAYQNAAYAERYGRMVAAVAGAEQRIAGEAGLLAEAVARSYYRVLA 1015

Query: 1004 YKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRF-GPWMF 1062
            YKDEYEVARL ++  F + +  TF+G  K  FH+APP L+      GR  K    G  M 
Sbjct: 1016 YKDEYEVARLHSDPAFARSLESTFDGHGKKTFHMAPPWLTRVDRNTGRRNKIVLSGTVMS 1075

Query: 1063 RAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAE 1122
               RLL   + LRGT  DPF   +DR+++R M+ + +  V  + R L+     +   L  
Sbjct: 1076 PLLRLLRHGKILRGTPFDPFGRQSDRRIERRMIVECEDDVQLVLRTLSERTLASAAALVG 1135

Query: 1123 LPADVRGYGPVREQAAESIREKQTQLIK 1150
              A +RG+G ++E+   + R  Q  L K
Sbjct: 1136 AYAQIRGFGVIKER---NYRSAQADLQK 1160


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: 3065
Number of extensions: 120
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: 1162
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1115
Effective search space:  1254375
Effective search space used:  1254375
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources