Alignments for a candidate for iorAB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Caulobacter crescentus NA1000

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate CCNA_03280 CCNA_03280 pyruvate ferredoxin/flavodoxin oxidoreductase family protein

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



>FitnessBrowser__Caulo:CCNA_03280
          Length = 1146

 Score =  968 bits (2503), Expect = 0.0
 Identities = 528/1150 (45%), Positives = 726/1150 (63%), Gaps = 31/1150 (2%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L+D+Y+ E GR F+TG QAL+R+ L +  LDRK GLNT G +SGYRGSPLG +DQ   + 
Sbjct: 8    LDDKYVLEDGRAFITGVQALLRVLLDRKRLDRKAGLNTGGYLSGYRGSPLGGLDQQAARI 67

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            K LL  + + F   +NEDLAAT + G+QQ         +GVFG+WYGK PGVDR GD  K
Sbjct: 68   KKLLTAHDVVFQEGLNEDLAATAVWGSQQANLFPGALYDGVFGMWYGKAPGVDRTGDVFK 127

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            H    G+ P GGVL VAGDDHGC SS++P QS+ AF  F MP ++PA++ E L++GL G 
Sbjct: 128  HANFAGTFPTGGVLAVAGDDHGCKSSTLPSQSEFAFQDFEMPVLSPADVQEVLDYGLLGI 187

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHYRWPDLPGPQLET 252
            ++SR+SG W G  A+++T++S  ++++      +   +F  P  GL  R  D P  +   
Sbjct: 188  SMSRFSGLWTGMIALADTMDSGVTIDVSLDRHQIVVPEFAFPPGGLGIRQKDQPMEKERR 247

Query: 253  RIEHKLAAVQAFARANRIDRCLFDNK-----EARFGIVTTGKGHLDLLEALDLLGIDEDK 307
               HK+ A  AFARAN IDR +         +AR GIV  G+ + D+LEA   +G+   +
Sbjct: 248  MRLHKIPAALAFARANNIDRVVLGASHVKVGKARLGIVCQGQAYKDVLEAFTAMGMTLQE 307

Query: 308  ARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEVL 367
            A D+G+ IYKVGM WPLE  G+  F  G E ++VIE KR +IE Q +  + +        
Sbjct: 308  AADLGVSIYKVGMPWPLEPLGLRAFAAGLETLMVIEHKRALIEPQARAALYDLPAQARPR 367

Query: 368  ITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVDFSE------RMAEISAMTTAQ 421
            + GK DE G PL+  +G LS   +A  +  RL +   ++ ++        A ++A++ A 
Sbjct: 368  VIGKTDEKGGPLLSELGSLSVAEIALAIYDRLPQGPHMERAQAYLNRVSAAGVAAVSLAA 427

Query: 422  DPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWI 481
            D     R P+FCSGCPHNTSTK+PEGS+ALAGIGCH+MA +    T+    MGGEG+ W+
Sbjct: 428  DQA---RKPFFCSGCPHNTSTKLPEGSRALAGIGCHYMAGFNDPMTDLNTHMGGEGLTWV 484

Query: 482  GKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQI 541
            G + +T   HVFQNLG+GTY HSGS+AIR AVAAG NITYK+L+NDAVAMTGGQ  +   
Sbjct: 485  GAAPFTSEKHVFQNLGDGTYNHSGSLAIRGAVAAGTNITYKLLYNDAVAMTGGQRAESGF 544

Query: 542  TVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCT 601
            T  +I +Q+AAEGV + V++ DE E+Y G +DL P  V    RS+L +VQ  LR+ PG T
Sbjct: 545  TPAQITRQLAAEGVKKTVIVVDELERYQGVNDLAP-GVEIFPRSDLMRVQEMLRETPGTT 603

Query: 602  VLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRK 661
            VL+YDQTCA EKRRRRKR   P   +R FIN  VCEGCGDCSV+SNC+SV P  TE GRK
Sbjct: 604  VLLYDQTCATEKRRRRKRGSMPKATQRVFINPLVCEGCGDCSVKSNCVSVEPLATEFGRK 663

Query: 662  RKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGS 721
            RKI+QSSCN+D+SCV GFCPSF+T+EG +  +S+   T + LT +    P P+   +TG 
Sbjct: 664  RKINQSSCNQDYSCVEGFCPSFITLEGAESAQSK--KTPAALTAE--STPLPEFEPLTGV 719

Query: 722  YDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLH 781
              +L  GVGGTGV TV  ++ MAAH++ R  SV+D  G AQKGG+V S+V++  + + + 
Sbjct: 720  RKILFTGVGGTGVTTVASIMAMAAHIDGRAGSVVDMTGLAQKGGSVFSHVKIGKTEETIV 779

Query: 782  QVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADK 841
              R+    AD +IACDL+VA+S + LS+   + TR   N    PTAD+V  RD    +  
Sbjct: 780  GGRVPAASADVLIACDLLVAASPEGLSLYAKDRTRAFGNSDFAPTADFVTSRDVRFDSGA 839

Query: 842  RLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIEL 901
                +K A     FD   A  +AE   GD +++N++M+GFAWQ+G++PLS  A+ +AI+L
Sbjct: 840  MARRVKGAT--KTFDACPAQRLAETEFGDAIYANMIMVGFAWQRGVIPLSSRAVYRAIKL 897

Query: 902  NGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNYQ 961
            NGV  + N +AF  GR  A DPS +T  + +      E  P   LD LI  R   L  YQ
Sbjct: 898  NGVDAEANLQAFELGRRVAHDPSTLT--VKEDTTPTPETMP---LDALIAHRIAQLTAYQ 952

Query: 962  NQRWADQYRDAVAGVRKAEESL-GETNLL-LTRAVAQQLYRFMAYKDEYEVARLFAETDF 1019
            N  +A +Y D VA VR AE ++ GE   L LTRA A  LY+ MAYKDEYEVARL+ +  F
Sbjct: 953  NAAYAQRYADKVAKVRAAETAVSGEDGALPLTRAAAVNLYKLMAYKDEYEVARLYTDGRF 1012

Query: 1020 MKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMF-RAFRLLAKLRGLRGTA 1078
              E+  TF+G  K    LAPPLL+ +    G+PKK  FG WM   AF ++AK++GLRGTA
Sbjct: 1013 AAELAGTFKGG-KAKVWLAPPLLAPK-GPDGKPKKIAFGGWMLDLAFPMMAKMKGLRGTA 1070

Query: 1079 IDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAA 1138
            +D F  + +R+++R ++  Y++ +DR+   L A +    +++AE+P  +RG+G V+E + 
Sbjct: 1071 LDIFGKTEERRMERGLIASYETGLDRLAAGLKAESLPLAVKIAEVPQAIRGFGHVKEASV 1130

Query: 1139 ESIREKQTQL 1148
             + +  + +L
Sbjct: 1131 VTAKAAEAKL 1140


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: 2948
Number of extensions: 138
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: 1146
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1099
Effective search space:  1236375
Effective search space used:  1236375
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