Alignments for a candidate for ofo in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Dinoroseobacter shibae DFL-12

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate 3608360 Dshi_1762 pyruvate ferredoxin/flavodoxin oxidoreductase (RefSeq)

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>FitnessBrowser__Dino:3608360
          Length = 1135

 Score = 1044 bits (2699), Expect = 0.0
 Identities = 557/1131 (49%), Positives = 745/1131 (65%), Gaps = 19/1131 (1%)

Query: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60
            MSL +IRL D+Y L    + L GTQAL RL ++Q  RD+A GLNTGG+++GYRGSPLG +
Sbjct: 1    MSLQDIRLSDRYDLDRETVLLNGTQALVRLTLMQAARDRAAGLNTGGYVTGYRGSPLGAV 60

Query: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120
            D+ +    D L++  + F+PG+NE+LAATA+WG+QQ  L      DGVF MWYGKGPGVD
Sbjct: 61   DQQMGRNLDLLREAGVIFEPGLNEDLAATALWGTQQAELRGEGSRDGVFGMWYGKGPGVD 120

Query: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180
            R+GDV KHAN AG SP GGVL + GDDH  +SST  HQSE A + A +PVL+PA VQEIL
Sbjct: 121  RSGDVMKHANLAGTSPHGGVLFVMGDDHTGESSTTCHQSEFALLDAYMPVLSPAGVQEIL 180

Query: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240
            DYG+ GW LSRY+G WV LK + + V+++AVV+    R++   P D+ +PE G++IR  D
Sbjct: 181  DYGLFGWALSRYAGVWVGLKAMKDTVEATAVVDGRADRMRFVTP-DYAMPEGGLNIRLVD 239

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
                QE+RL  +K YAA AF  AN +++ ML  P  ++G +  GK++LD+  ALD LG+D
Sbjct: 240  HWTPQEERLIAHKRYAAEAFGHANGIDKRMLGKPGAKIGFLAAGKNWLDLAHALDLLGID 299

Query: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360
             A   ++G+   KVGM+WPL+      +A+GLD I+VVEEKR ++E Q+   ++N    +
Sbjct: 300  GARAEALGITAYKVGMTWPLDVKGFLGWAEGLDVIVVVEEKRKLLEVQVKEAIFN--DRR 357

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPI-YTSDSIQARLAFLAAKEKALA 419
              RV G     G  L P    L P  IA  + + L      S+ ++ARLA LA   +A  
Sbjct: 358  GRRVYGGQKAPGEVLFPAYGALDPVTIAEKLGQILIEEGRASEDLEARLARLAEVRRADN 417

Query: 420  ARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNW 479
            A+  +  RTP++CSGCPHN+ST+VPEG+ A AGIGCH M  WMDR T  +T MG EG NW
Sbjct: 418  AKDLA-ARTPYFCSGCPHNTSTRVPEGAIAYAGIGCHVMAMWMDRDTNGYTHMGAEGANW 476

Query: 480  IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539
            IG+  F+   H+FQNLGDGTY HSG  A+RAA AA  N+TYKIL+NDAVAMTGGQ  DG 
Sbjct: 477  IGEGKFSTRSHVFQNLGDGTYNHSGIQAIRAAHAAKANITYKILFNDAVAMTGGQTNDGG 536

Query: 540  LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599
            L   +++ ++   G++ I +V DE ++      F P    H R EL  VQ EL++ +G +
Sbjct: 537  LDAARIAWELKGIGLRDIRIVYDEKEEV-DFSAFPPDLPRHGRDELMTVQEELQQVRGTT 595

Query: 600  VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659
             I+Y QTCA EKRRRRKRG   DP KR FIN  VCEGCGDCG +SNC+A++P ETELGRK
Sbjct: 596  AILYIQTCAAEKRRRRKRGTFPDPDKRVFINTDVCEGCGDCGVQSNCVAIVPAETELGRK 655

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVL 719
            R +DQ+ACNKDFSC++GFCPSFVTV G   RK  A    ++   LP+P  P +D   N+L
Sbjct: 656  RAVDQSACNKDFSCLKGFCPSFVTVSGARPRK--AATAEVDLGHLPDPALPAIDGTHNLL 713

Query: 720  IPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRI 779
            I GVGG GV T+GA L MAAHLEGKG  +++ AGLAQK G V  H RIAA+  DI AVR+
Sbjct: 714  ITGVGGMGVVTIGATLAMAAHLEGKGVGMMEMAGLAQKGGAVQIHCRIAARPEDITAVRV 773

Query: 780  AAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQA 839
            + GEA  ++G DL+V    +    + +  + AVVNSHE  T  FTR+ + ++PGA ++ +
Sbjct: 774  SVGEAHGVIGGDLVVTGAGKIQGMMAKGRTGAVVNSHEIVTGAFTRDREFRIPGADLQVS 833

Query: 840  ISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVS 899
            +   +GA+   F DA+ LA ++LGD+I +N+ + G A+Q+GL+P+  +AI +AI+LNG +
Sbjct: 834  LQARLGAEAVVFFDASELAQKVLGDAIFSNMVVTGAAWQRGLIPLGRDAIFQAIKLNGAA 893

Query: 900  AKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARR 959
               N QAF  GR AVL  EAV ++        P  K+L E +D+R D L  YQSA LA++
Sbjct: 894  PDRNKQAFDLGRWAVLNPEAVAKMLAAEVTARP--KSLAEKIDFRADHLRAYQSARLAKK 951

Query: 960  YRQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDY 1019
            YR+ VE V D D      L   VA+ Y KLL+YKDEYEV+RL  +   R + EA FEG+ 
Sbjct: 952  YRRAVEAVTDPD------LRAVVAQNYHKLLSYKDEYEVSRLLRDT--RAKAEAAFEGEL 1003

Query: 1020 KLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVE 1079
            +L +HLAP  L++  P  G PRKR  G W+   +G LA  + LRGTPLDPFGY  +RR+E
Sbjct: 1004 ELTYHLAPPLLSRAGP-DGRPRKRAFGSWIEKAYGPLAALKLLRGTPLDPFGYTAERRME 1062

Query: 1080 RQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKAR 1130
            R+LI  YE  +  + A++ P     A A+ A P+ +RG+GPVK +++   R
Sbjct: 1063 RELIRLYEADLARVQAEMTPARAEAARALLAWPDMVRGFGPVKAQAVETMR 1113


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: 2842
Number of extensions: 121
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: 1156
Length of database: 1135
Length adjustment: 46
Effective length of query: 1110
Effective length of database: 1089
Effective search space:  1208790
Effective search space used:  1208790
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 (21.8 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