Alignments for a candidate for ofo in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Cupriavidus basilensis 4G11

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate RR42_RS10350 RR42_RS10350 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Cup4G11:RR42_RS10350
          Length = 1162

 Score = 1004 bits (2597), Expect = 0.0
 Identities = 549/1177 (46%), Positives = 735/1177 (62%), Gaps = 59/1177 (5%)

Query: 22   LEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWKA 81
            LED+Y  E G V+++GTQALVR+ + Q   DR AGL T G +SGYRGSPLG  DQ LW+ 
Sbjct: 7    LEDRYRREAGSVFLTGTQALVRILVEQARADRIAGLKTGGLVSGYRGSPLGGFDQELWRQ 66

Query: 82   KQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVFK 141
            +  LA ++I F+ GLNEDL AT +WG+QQ++ +P  R EGVF MWYGKGPGVDRT DVF+
Sbjct: 67   RSLLAEYEIRFEPGLNEDLGATMLWGAQQIDAFPGKRVEGVFSMWYGKGPGVDRTGDVFR 126

Query: 142  HANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHAW 201
            +AN  G+SRHGGVL +AGDDHAA+SS   HQ++H+F+   +PVL+P++V+EY+++GL  +
Sbjct: 127  NANVLGTSRHGGVLAIAGDDHAAQSSMFPHQTDHVFEGAMMPVLFPASVEEYVEFGLFGY 186

Query: 202  AMSRYSGLWVSMKCVTDVVESSASVEL----DPHRVEIVLPQDFILPPGGLN----IRWP 253
            A+SR+SGLWV+ K +T+ VES  S+ +            LP D  +P  G      ++WP
Sbjct: 187  ALSRFSGLWVAFKAITETVESGRSMLIGGAGSARGARFSLPGDIDIPERGFGYDTGVKWP 246

Query: 254  DPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGL 313
                E E RLL+ +  A  A+ RAN IDR  +    AR GI+T GKA+ D   ALA LGL
Sbjct: 247  GQRAELERRLLEERLPAAQAFARANPIDRTIVRPRDARIGIVTVGKAHGDLLAALARLGL 306

Query: 314  DDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDD 373
            D+   A +GI LYK+G  WP+E  G R FA G++ +LVVEEKR  +E  ++E L+N    
Sbjct: 307  DEPRLAELGIGLYKIGMTWPIEGEGVRRFASGMRALLVVEEKRSFVERQIQETLFNVAAP 366

Query: 374  VRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARI 433
             RP+V+GK    D             LLPA  E +P  + +A    L +F     V A  
Sbjct: 367  QRPEVFGKRGPNDAP-----------LLPATLEFAPDQLQKA----LRQFLAYTGVHALP 411

Query: 434  AARIAVIEAKEKAMAVPRVAAE-------RKPWFCSGCPHNTSTNVPEGSRALAGIGCHY 486
                    A  +   V  ++A+       RKP+FC+GCPHN+ST +P+GS A AGIGCH 
Sbjct: 412  PGNTGSAAALPRQPRVIPLSAQLQPDVLTRKPFFCAGCPHNSSTKLPDGSYAAAGIGCHI 471

Query: 487  MTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVN 546
            M +    +T+TF QMGGEGV W+G + F+   H+F NLGDGTY HSG LAIR ++AAG  
Sbjct: 472  MALGQGDNTATFCQMGGEGVQWVGLSSFSDLPHLFVNLGDGTYQHSGSLAIRQAVAAGTA 531

Query: 547  ITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGV 606
            +TYKIL+NDAVAMTGGQP +G L+V  +  Q+ AEG  K+V+V+D P++Y  A  +P  V
Sbjct: 532  VTYKILFNDAVAMTGGQPTEGGLTVPRMVAQLIAEGVGKVVLVSDHPQRYWGAKSIPASV 591

Query: 607  EVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGC 666
            E+ HRD LD +QR LR   G + ++YDQTCA EKRRRRKRGT  DP +R  IN +VCEGC
Sbjct: 592  EIAHRDALDDVQRRLRAYRGVSAIVYDQTCAAEKRRRRKRGTLADPVRRVVINPSVCEGC 651

Query: 667  GDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGV 726
            GDCSV+SNC+++EPLET LG KR +NQSSCNKD SC+ GFCPSFVT EG Q K+  +  +
Sbjct: 652  GDCSVQSNCIAIEPLETPLGRKRAVNQSSCNKDMSCLKGFCPSFVTIEGLQPKRANQRRI 711

Query: 727  SMDNL---PALPQPALPG-----LEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTV 778
                     +LP PA P      LEH   +LVTGVGGTGVVT+G +L MAAHLE KG   
Sbjct: 712  QQMEAQWRASLPPPAGPAALGALLEHA-RILVTGVGGTGVVTVGAILAMAAHLEGKGAAT 770

Query: 779  LDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGR 838
            LD  GLAQK GAV+SHVQ+A   +++   RI    AD++IGCDA+V+A  DV+++ +   
Sbjct: 771  LDFTGLAQKNGAVVSHVQLADRRERIVTARIEACSADVMIGCDAVVAASPDVLARLRKCG 830

Query: 839  TRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEA-CDFINASGLAVALIGDAIFT 897
            TRA+VN+A  PTA+F+ N          +  + + VG    +F + +  A+ L GDAI T
Sbjct: 831  TRAVVNSAVAPTADFVANGDLPISREIHQAAIESVVGAGQAEFFDCTAAAMTLFGDAIAT 890

Query: 898  NPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLR 957
            N +++G+A+Q+GW+PLS  A+ RAIELNG AVE N+ AF WGR +A +P         LR
Sbjct: 891  NMMLVGHAYQRGWIPLSEMAIARAIELNGAAVELNRRAFLWGRILACEP-------NALR 943

Query: 958  NTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNG 1017
             T+        P      L + +A R   L+AYQ+AAYA+ +   V+ V  AE  + G  
Sbjct: 944  RTSAAEAQAAQPFE----LARFVAERKRDLSAYQNAAYAERYGRMVAAVAGAEQRIAGEA 999

Query: 1018 KPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPL 1077
                L EA AR+  +++AYKDEYEVARL++DP F   L + F+G   +     F +APP 
Sbjct: 1000 G--LLAEAVARSYYRVLAYKDEYEVARLHSDPAFARSLESTFDGHGKK----TFHMAPPW 1053

Query: 1078 MAKRDEK-GHLVKRRFGPSTMK-LFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRA 1135
            + + D   G   K     + M  L  +L   K LRG  FD FG+ ++RR ER +I E   
Sbjct: 1054 LTRVDRNTGRRNKIVLSGTVMSPLLRLLRHGKILRGTPFDPFGRQSDRRIERRMIVECED 1113

Query: 1136 LLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDN 1172
             ++ + R LS    A+A  L      IRGFG +K+ N
Sbjct: 1114 DVQLVLRTLSERTLASAAALVGAYAQIRGFGVIKERN 1150


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: 3135
Number of extensions: 144
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: 1197
Length of database: 1162
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1115
Effective search space:  1282250
Effective search space used:  1282250
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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Protein sequences (fasta format)
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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