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 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_011842516.1 RSPH17029_RS18350 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000015985.1:WP_011842516.1
          Length = 1119

 Score =  957 bits (2474), Expect = 0.0
 Identities = 531/1163 (45%), Positives = 710/1163 (61%), Gaps = 64/1163 (5%)

Query: 21   SLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWK 80
            +L D+YT   GR+  SG QAL RL + Q+ RDRA GL+TAG+++GYRGSPL   D  L +
Sbjct: 13   ALTDRYTQASGRILASGAQALARLMIEQQRRDRADGLDTAGYVTGYRGSPLADFDGELMR 72

Query: 81   AKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVF 140
            A + L+A  I FQ GLNEDLAAT+VWGSQQ+++ P AR +GVF +WYGKGPG+DR+ D  
Sbjct: 73   AGRFLSASAIRFQPGLNEDLAATAVWGSQQIDLSPGARHDGVFALWYGKGPGIDRSMDAI 132

Query: 141  KHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHA 200
            +HAN+AG+   GGVL+L GDDH A SST  HQSE +  +  +P+L P+ V+EY+D+GL  
Sbjct: 133  RHANAAGTHPRGGVLLLMGDDHGAVSSTFPHQSEQVLISAMVPILSPAGVEEYIDFGLAG 192

Query: 201  WAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQE 260
            +A+SR++G+WV  KC TD+VE + S++L        LP D  LPPGGL+IRWPD  L QE
Sbjct: 193  FALSRFAGVWVGFKCQTDIVECTRSIDLPDPAARPALP-DMTLPPGGLSIRWPDDKLAQE 251

Query: 261  ARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCAR 320
            AR L+ K  A  A+  AN +DRI      AR GI+  GKA+ D   A A  G+  E    
Sbjct: 252  AR-LEVKMEAVRAFAAANGLDRILGAGAGARRGIVATGKAWRDLTGAFARAGISPE---E 307

Query: 321  IGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVYG 380
             G+RL KVG +WPL       FAEGL+EILV+EEKR ++E  ++ + YN R   RP+++G
Sbjct: 308  AGLRLLKVGLLWPLVPATLERFAEGLEEILVIEEKRPVIEDQIRAQFYN-RTGARPRIWG 366

Query: 381  KFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIAT--RLDKFELPADVRARIAARIA 438
            K           + P+   L+ +  EL PA +   +A   RL    LP            
Sbjct: 367  K-----------TTPEGAPLISSTAELDPAGLVPVLAAFLRLPPMTLP------------ 403

Query: 439  VIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTSTF 498
              EA   A  +P     R+P+FCSGCPH+ ST +P+GSRA AGIGC  + V MDR+  TF
Sbjct: 404  --EAPAPAPGLP----FREPYFCSGCPHSVSTKLPDGSRATAGIGCSMLAVAMDRNVETF 457

Query: 499  SQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAVA 558
            +QMGGEG  WIG APF  ++HVF ++GDGTYFHSGLLAIRA++AAGVN TYKIL+NDAVA
Sbjct: 458  TQMGGEGANWIGHAPFTDERHVFVHMGDGTYFHSGLLAIRAAVAAGVNATYKILFNDAVA 517

Query: 559  MTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRIQ 618
            MTGGQ  DG L+V    +Q+ AEG R++VV+ +EP ++    +LP+GV+V HRD L   Q
Sbjct: 518  MTGGQTHDGSLTVPAAVDQIRAEGVRELVVIAEEPAQWRG--RLPEGVKVLHRDRLQAEQ 575

Query: 619  RELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSV 678
              LREV G T +IYDQ CA EKRRRRKRG++P PA +  I+  VCEGCGDCSV+SNC+++
Sbjct: 576  IRLREVEGVTCIIYDQVCAAEKRRRRKRGSHPKPAAQVMIHPGVCEGCGDCSVQSNCIAI 635

Query: 679  EPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQPA 738
            EPLET+LG KRQ+N S+CN D SC+ GFCPSFVT EG Q ++P+   +       LP P 
Sbjct: 636  EPLETDLGRKRQVNLSACNADLSCLKGFCPSFVTIEGGQ-RRPQLAPLPEALGHDLPPPV 694

Query: 739  LPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIA 798
                     +L+ G+GGTGV+T+  +L  AAHL+   V VL+  GLAQK GAV++H++ A
Sbjct: 695  ATTAGPAQALLLAGIGGTGVITVSAILAQAAHLDGLAVQVLNQTGLAQKNGAVMAHLRFA 754

Query: 799  AHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPK 858
                 LHA RI + EAD V+  D++ +A    ++    GRTR + +   TPTA F+++  
Sbjct: 755  TDARALHAPRIGLAEADAVLAFDSVAAAAPKGLACIDPGRTRVVADRHVTPTAGFVRHST 814

Query: 859  WQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDAL 918
                   A   +R+  G   + + A+ LA+   GDAI  N L+ G+A+Q G +PLS  A+
Sbjct: 815  APREDTRAMDQLRSRAGARLETVPATELALRHFGDAIAANILLTGHAFQLGLIPLSEGAI 874

Query: 919  VRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGALLEK 978
            ++AI +NG A E+N  AF  GR +A  PE                     P ++   + +
Sbjct: 875  LQAIRMNGGAAERNLEAFRAGRLLAARPE----------------AFAPAPPAAEPTVAE 918

Query: 979  LIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKD 1038
            L      HLT +QDA YA  F   V R  A      G    L    A  R    +MA+KD
Sbjct: 919  LRDRLVRHLTEWQDARYAARFERLVDRAAARVQGWTGGEAFL---RALMRGTHHVMAFKD 975

Query: 1039 EYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEK-GHLVKRRFGPSTM 1097
            EYEVARL+ DP F   +  +FEG    DY++ + L+PP   + D + G   K RFGP   
Sbjct: 976  EYEVARLHLDPAFHASVAREFEG----DYRIAYHLSPPFPGRTDARTGRPAKLRFGPWMQ 1031

Query: 1098 KLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAITLAS 1157
              F +LA++K LRG  FD FG+++ERR ERAL   Y   +EEL   L+  +   A   A 
Sbjct: 1032 HGFRLLARMKRLRGTPFDPFGQSSERRAERALRERYIRRMEELLAALTPEDLPAATQEAE 1091

Query: 1158 LPDDIRGFGHVKDDNLAKVRTRW 1180
                +RGFG VK  NLA+ +  W
Sbjct: 1092 AVLAVRGFGPVKAGNLARWQAEW 1114


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: 3198
Number of extensions: 166
Number of successful extensions: 11
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: 1119
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1072
Effective search space:  1232800
Effective search space used:  1232800
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 Apr 10 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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