Alignments for a candidate for ofo in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Cereibacter sphaeroides ATCC 17029

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 WP_011841122.1 RSPH17029_RS08070 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000015985.1:WP_011841122.1
          Length = 1128

 Score = 1053 bits (2724), Expect = 0.0
 Identities = 571/1146 (49%), Positives = 764/1146 (66%), Gaps = 30/1146 (2%)

Query: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60
            MS  +++L D+  L+   + L GTQA+ RL ++Q  RD+A G NT G+++GYRGSPLG +
Sbjct: 1    MSRQDVKLSDRTDLSKSPVLLNGTQAMVRLMLMQKARDRAEGRNTAGYVTGYRGSPLGAV 60

Query: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120
            D ++  A   LK   I FQPG+NE+LAATAVWGSQQ  L    ++DGVFA+WYGKGPGVD
Sbjct: 61   DLTMARAEKDLKAADILFQPGLNEDLAATAVWGSQQAELRGEGRFDGVFALWYGKGPGVD 120

Query: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180
            R GDV +HAN AG SP GGVL+  GDDH  +SST  HQS+ A + A IPVL+PA VQEIL
Sbjct: 121  RTGDVMRHANMAGTSPWGGVLMAMGDDHTGESSTTLHQSDWAMVDAYIPVLSPAGVQEIL 180

Query: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240
            DYG+ GW LSR++G WV LKT+ + V+++AVV+  P R+Q   PE F +PE G++IR  D
Sbjct: 181  DYGLYGWALSRFAGVWVGLKTMKDTVEATAVVDGRPDRMQFVRPE-FRMPEGGLNIRLVD 239

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
             P+AQE R+  +K +AA AF+ AN ++R +   P  ++G ++ GKS+LD+  AL  LG+ 
Sbjct: 240  TPVAQEARMIDHKRFAAEAFSHANGMDRRVWGRPGAKIGFVSAGKSWLDLVHALSLLGVG 299

Query: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360
            EA    +G+   KVG  WP++     ++A+GLD I+ VEEKR +IE Q    ++N    +
Sbjct: 300  EAEAERLGITTYKVGQVWPMDFRGFRDWAEGLDLIVCVEEKRKLIEVQAKEAIFN--DRR 357

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPI-YTSDSIQARLAFLAAKEKALA 419
              R+ G  +++G  L P    L P  IA  I K L      +D ++A LA LA   +A  
Sbjct: 358  GRRIYGWQNDRGEELFPTRYALDPIGIAEKIGKILIEEGRGTDRVKAGLAQLAEARRADN 417

Query: 420  ARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNW 479
            A+  +  R P++CSGCPHNSST++PEGSRA AGIGCHYMVQWMDR T  FTQMGGEG NW
Sbjct: 418  AQDLA-ARLPYFCSGCPHNSSTRLPEGSRAYAGIGCHYMVQWMDRDTVGFTQMGGEGANW 476

Query: 480  IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539
            IG+APF+  PH+FQNLGDGTY HSG  A+RAA+AAG  +TYKIL+NDAVAMTGGQ  +G 
Sbjct: 477  IGEAPFSKRPHVFQNLGDGTYNHSGVQAIRAALAAGTTITYKILFNDAVAMTGGQTNEGG 536

Query: 540  LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599
            L  D++ R+I   GVKRIA+V D  ++      F      H R E+ AVQR+    +GVS
Sbjct: 537  LSADRIVREIQAMGVKRIAVVHDAKEEV-DLSRFPSGIEIHERAEMMAVQRDFATVEGVS 595

Query: 600  VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659
             I+Y QTCA EKRRRRKRG   D  KR FIN  VCEGCGDCG +SNC++++P+ETELGRK
Sbjct: 596  AIVYIQTCAAEKRRRRKRGTFPDIDKRVFINTEVCEGCGDCGVQSNCVSIVPVETELGRK 655

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVL 719
            R IDQ++CNKDFSC+EGFCPSFVT+ G   +K  A    IE   LPEP  P +   +N+L
Sbjct: 656  RAIDQSSCNKDFSCLEGFCPSFVTLEGAKPKK--AATAEIELPDLPEPDLPAIRGSYNLL 713

Query: 720  IPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRI 779
            + GVGG+GV T+GA+L MAAHL+G+G  +++ AGLAQK G V  H RIA K SDI A+R+
Sbjct: 714  VTGVGGTGVVTVGAILSMAAHLDGRGAAMMEMAGLAQKGGAVQIHCRIAEKPSDISAIRV 773

Query: 780  AAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQA 839
            A GEAD ++G DL+V AG ++L  +++  + AVVNSH+  T EFTRN D +VP   ++ +
Sbjct: 774  AVGEADGVIGGDLVVTAGAKTLGLMSQGRTGAVVNSHDIVTGEFTRNTDFRVPSDRLQVS 833

Query: 840  ISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVS 899
            +   +  D+  F+DAT LA  L+GDSI +N+ + G A+Q+GL+P+SAEAI++AIELNG +
Sbjct: 834  LQARL-QDRVAFLDATELARILMGDSIYSNMMVFGAAWQRGLIPLSAEAIQRAIELNGAA 892

Query: 900  AKLNLQAFRWGRRAVLEREAVEQ--LARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLA 957
               N +AF  GR AVL     ++  L  P   V+P+         +R + L  YQS  LA
Sbjct: 893  VAQNARAFTLGRWAVLHPAEADRILLPEPPAPVDPVA--------YRAERLVGYQSRRLA 944

Query: 958  RRYRQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEG 1017
            RR+R LV      DSA    + + VAR Y++LLAYKDEYEVARL+ +    ++ +A+F+G
Sbjct: 945  RRFRTLV------DSAPP-EIREDVARGYYQLLAYKDEYEVARLHLDT--LERAKAEFDG 995

Query: 1018 DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRR 1077
            D++  FHLAP +LA +      P+KR  G W+L  F +LA  + LRGT LDPF    +R+
Sbjct: 996  DFRPTFHLAPPFLAGKG--EERPKKRAFGRWMLPAFRLLAALKPLRGTALDPFARNPERQ 1053

Query: 1078 VERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLR 1137
            +ER+LI+E+E  + E L QL+P        +A LP  IRGYGPVKE +   A  + + L 
Sbjct: 1054 LERRLIAEFEDDMAEFLPQLRPETMELGRELARLPLSIRGYGPVKEANATTAALRREALL 1113

Query: 1138 EQLAKG 1143
              +  G
Sbjct: 1114 AAIRAG 1119


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: 2856
Number of extensions: 120
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: 1156
Length of database: 1128
Length adjustment: 46
Effective length of query: 1110
Effective length of database: 1082
Effective search space:  1201020
Effective search space used:  1201020
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 Apr 10 2024. 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