Alignments for a candidate for ofo in Dokdonella koreensis DS-123

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Dokdonella koreensis DS-123

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_067647538.1 I596_RS10685 indolepyruvate ferredoxin oxidoreductase family protein

Query= reanno::Cup4G11:RR42_RS19540
         (1197 letters)



>NCBI__GCF_001632775.1:WP_067647538.1
          Length = 1189

 Score = 1288 bits (3332), Expect = 0.0
 Identities = 671/1201 (55%), Positives = 823/1201 (68%), Gaps = 48/1201 (3%)

Query: 21   SLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWK 80
            +L+ KYT   GR+Y+SG QALVRLP++Q+ RDRAAG+NTAGFISGYRGSPLG  D  LWK
Sbjct: 13   TLDHKYTRSEGRIYLSGVQALVRLPLMQQMRDRAAGVNTAGFISGYRGSPLGGFDLELWK 72

Query: 81   AKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVF 140
            A++HL A  I F  GLNEDL AT VWG+QQ N++P A+ +GVF MWYGKGPGVDR  DVF
Sbjct: 73   ARKHLKASAIEFTPGLNEDLGATMVWGTQQTNLFPGAKVDGVFAMWYGKGPGVDRCGDVF 132

Query: 141  KHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHA 200
            KH N+AG+SRHGGVL LA DDHA +SSTL H SE  F +  +P+L P+ VQ+ LD GL  
Sbjct: 133  KHGNAAGTSRHGGVLALAADDHACRSSTLPHGSELEFVSAMMPILNPAGVQDILDMGLLG 192

Query: 201  WAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQE 260
            WAMSR++G WV  K + + VESSASV ++PH+++IVLP+DF LPPGGLNIRWPDPPL+QE
Sbjct: 193  WAMSRFTGRWVGFKTIAETVESSASVNVNPHQLDIVLPEDFALPPGGLNIRWPDPPLDQE 252

Query: 261  ARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCAR 320
             RL  Y   A  A+ RAN+IDRI +DSP AR GI+T GK+YLD  QAL  LG+ +     
Sbjct: 253  MRLHRYAVQAATAFARANRIDRIVLDSPKARLGIVTTGKSYLDVLQALEYLGISERDARE 312

Query: 321  IGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVYG 380
            IGIR+YK+G  WPLE  G R FA+GL++++VVEEKR  +E  +KE +YNW    RP V G
Sbjct: 313  IGIRVYKIGMTWPLEPVGIRQFADGLEDVIVVEEKRSFIESQMKEYMYNW--PTRPSVVG 370

Query: 381  KFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAARIAVI 440
            K+DE             NW+LP+  EL+PA+IA  IA RL +F     +R    AR+A I
Sbjct: 371  KYDE-----------DGNWVLPSTNELTPAMIALVIARRLSRFFSSEAIR----ARVAWI 415

Query: 441  EAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTSTFSQ 500
            EAKE+ + +PR    R   +CSGCPHNTST VPEGSRA  GIGCHYM  WMDR T TFS 
Sbjct: 416  EAKEQELTLPRANFPRAAHYCSGCPHNTSTAVPEGSRAQGGIGCHYMVTWMDRRTDTFSH 475

Query: 501  MGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAVAMT 560
            MGGEGV W GQAPF   +HVF NLGDGTYFHSG LAIR +IAA VNITYKILYNDAVAMT
Sbjct: 476  MGGEGVTWCGQAPFTETEHVFQNLGDGTYFHSGSLAIRQAIAAKVNITYKILYNDAVAMT 535

Query: 561  GGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRIQRE 620
            GGQP+DG L+V D+A+Q+ AEG + I+VV+D+  K+S     P GVE  HRDELD +Q+ 
Sbjct: 536  GGQPVDGTLTVPDIAHQMRAEGVQAIIVVSDDIAKWSRPEIFPSGVEFVHRDELDAVQKR 595

Query: 621  LREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSVEP 680
            +R++ G +ILIYDQTCATEKRRRRKRG   DP KR FIN  VCEGCGDC  KS C+SV P
Sbjct: 596  MRQIKGVSILIYDQTCATEKRRRRKRGKLEDPKKRVFINSLVCEGCGDCGAKSFCVSVLP 655

Query: 681  LETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQPAL- 739
             ETE G KR+I+QS CNKD+SCV GFCPSFVT  G  ++K +  G ++D   ALP P   
Sbjct: 656  KETEYGRKREIDQSGCNKDYSCVKGFCPSFVTVHGGGLRKKKGSGGAVD-FGALPMPVFA 714

Query: 740  PGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIAA 799
              L+ P+ +LVTG+GGTGVVTIG L+GMAAHLE KG TVLD  GLAQKGGAV  H++IA 
Sbjct: 715  TALDQPWNILVTGIGGTGVVTIGALIGMAAHLEGKGSTVLDQTGLAQKGGAVTCHLRIAK 774

Query: 800  HPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPKW 859
             P  +HA RIA GEADLV+GCD +V      +SK + GR+  ++N+ +     F   P  
Sbjct: 775  SPADIHAVRIAAGEADLVLGCDMVVVNDYWALSKIRAGRSNVVLNSYEAMPGTFTTKPDL 834

Query: 860  QFPGLSAEQDVRNAV-GEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDAL 918
             FP       V+ A+ G A + ++A+ LA AL+GD I  N  +LGYAWQKGW+PLSLDAL
Sbjct: 835  VFPAQKIIDSVKLALDGRAPELVDATELATALLGDTIAANLFMLGYAWQKGWVPLSLDAL 894

Query: 919  VRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLP--TSSGAL- 975
            +RAIELNG A+E N AAF+WGR  AHD   V +  G   +   GA  + LP   ++GA  
Sbjct: 895  MRAIELNGAAIEMNTAAFNWGRLGAHDIGQVRAAAGIKPHLPSGAIPLALPIRPAAGAAV 954

Query: 976  -------------------LEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGN 1016
                               L++ IA R   LT YQ+AAYA  +   V RVRAAE      
Sbjct: 955  PSPAAAGADALDDVALSVDLDEAIARRRTFLTDYQNAAYAGRYAALVERVRAAEQQAAPG 1014

Query: 1017 GKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPP 1076
             K   LTEA AR   KLMAYKDEYEVARLYT   F  ++R  FEG    DY ++F LAPP
Sbjct: 1015 TK--ALTEAVARYAFKLMAYKDEYEVARLYTRGDFEQRIRETFEG----DYTIHFHLAPP 1068

Query: 1077 LMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRAL 1136
            L+A++D +GHL K  +GP     F VLA+LKGLRG   D+FG TAER+ ER LI +Y   
Sbjct: 1069 LLARKDAEGHLRKAEYGPWVFTAFRVLARLKGLRGTPLDLFGYTAERKMERRLIEDYFRQ 1128

Query: 1137 LEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQRV 1196
            +EEL  GL   NHA A+ +AS+P+ IRG+GHVK+ +LA    R   LL  +R+P  A+  
Sbjct: 1129 VEELLAGLDRDNHALAVDIASVPELIRGYGHVKERHLADAMKRQDDLLAAWRNPAGARAA 1188

Query: 1197 A 1197
            A
Sbjct: 1189 A 1189


Lambda     K      H
   0.319    0.135    0.407 

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: 3324
Number of extensions: 124
Number of successful extensions: 9
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: 1197
Length of database: 1189
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1142
Effective search space:  1313300
Effective search space used:  1313300
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: 59 (27.3 bits)

This GapMind analysis is from Sep 24 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