Alignments for a candidate for ofo in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Dechlorosoma suillum PS

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate Dsui_0379 Dsui_0379 indolepyruvate ferredoxin oxidreductase, alpha/beta subunit

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



>FitnessBrowser__PS:Dsui_0379
          Length = 1183

 Score = 1429 bits (3698), Expect = 0.0
 Identities = 724/1186 (61%), Positives = 882/1186 (74%), Gaps = 32/1186 (2%)

Query: 13   IRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLG 72
            + + LA+ SL+DKYT   GR +++GTQAL+RLPMLQR RD+A GLNTAGFISGYRGSPLG
Sbjct: 8    VPKELASASLDDKYTTLSGRAFLTGTQALIRLPMLQRLRDQAQGLNTAGFISGYRGSPLG 67

Query: 73   ALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPG 132
             LDQ LWKA+++LA + I FQ G+NEDLAAT+VWGSQQVN++P A+++GVF +WYGKGPG
Sbjct: 68   GLDQGLWKAQKYLAENHITFQPGVNEDLAATAVWGSQQVNLFPGAKYDGVFALWYGKGPG 127

Query: 133  VDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQE 192
            VDR+ DVF+HAN+AGSSRHGGVLV+AGDDHAAKSSTL HQ+EH+FKA  +PVLYP+NVQE
Sbjct: 128  VDRSGDVFRHANAAGSSRHGGVLVVAGDDHAAKSSTLPHQTEHVFKAVMMPVLYPANVQE 187

Query: 193  YLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRW 252
            YL+YGLH WAMSRYSG WV+ K + D VE+SASV +DP  ++I LP DF LP  GLNIRW
Sbjct: 188  YLEYGLHGWAMSRYSGCWVAFKALADTVETSASVWVDPMALDIRLPDDFELPADGLNIRW 247

Query: 253  PDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLG 312
            PDPPL QEARL  +K YA LAY RAN+++RI IDSP  R GI+T GK+YLD  QAL  LG
Sbjct: 248  PDPPLVQEARLTHFKLYAALAYARANRLNRIVIDSPAPRLGIITAGKSYLDVMQALDELG 307

Query: 313  LDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRD 372
            +D +  A+IGIRLYKVG VWPLE+ G R FAEGL EILVVEEKRQ++EY LKEELYNWR+
Sbjct: 308  IDQQLAAQIGIRLYKVGMVWPLESEGVRQFAEGLDEILVVEEKRQMLEYQLKEELYNWRE 367

Query: 373  DVRPKVYGKFDEKDNAGGEWSI--------PQSNWLLPAHYELSPAIIARAIATRLDK-F 423
            DVRP+V GKFDEK    GEW++           +WLLPA  ELS A IARAIA+R+++ F
Sbjct: 368  DVRPRVVGKFDEK----GEWALLPDGKGHLAHGDWLLPAAGELSVAQIARAIASRIERHF 423

Query: 424  ELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIG 483
              PA     I AR+ +IEAK+KA+  P +  +R P FCSGCPHNTST VPEGSRA+AGIG
Sbjct: 424  TSPA-----IKARLDLIEAKQKALQTPLILTQRTPHFCSGCPHNTSTRVPEGSRAVAGIG 478

Query: 484  CHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAA 543
            CHYM  WMDRSTSTF+ MGGEGV W+GQAPF  +KH+FANLGDGTYFHSGLLAIR S+AA
Sbjct: 479  CHYMVTWMDRSTSTFTHMGGEGVTWVGQAPFTEEKHIFANLGDGTYFHSGLLAIRQSVAA 538

Query: 544  GVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLP 603
              NITYKILYNDAVAMTGGQP+DG LSV  +  Q+ AEG  ++V+VTDEPEKY+    L 
Sbjct: 539  KTNITYKILYNDAVAMTGGQPVDGILSVPRITRQLEAEGVGRMVIVTDEPEKYAEVTDLA 598

Query: 604  QGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVC 663
              V V HRDELD +QRELRE+PG TILIYDQTCATEKRRRRKRG   D  +R FIN+AVC
Sbjct: 599  PNVPVRHRDELDAVQRELREIPGTTILIYDQTCATEKRRRRKRGKLADVDRRVFINEAVC 658

Query: 664  EGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPER 723
            EGCGDCSV+SNCLSV P+ET+ G KR I+QS+CNKDFSC+ GFCPSFVT EGA++KK + 
Sbjct: 659  EGCGDCSVQSNCLSVIPVETDFGRKRAIDQSNCNKDFSCLKGFCPSFVTLEGAKLKKGQA 718

Query: 724  HGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAG 783
              +   + P LP+P LP    PY +LVTGVGGTGVVT+G L+GMAAHL+ KGV+VLDM G
Sbjct: 719  LAMDAQDWPPLPEPVLPPTARPYNLLVTGVGGTGVVTLGALIGMAAHLDGKGVSVLDMTG 778

Query: 784  LAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIV 843
            LAQK GAV +H++ A  P+ +HA RIA GEAD ++G D +V+A ++ +SK   GRTRA+V
Sbjct: 779  LAQKYGAVFTHLRFADRPEDIHAARIATGEADAILGGDVVVTAGNEALSKMLEGRTRAVV 838

Query: 844  NTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFTNPLVL 902
            N  +TPTAEF +NP WQFP    +Q V   VG +   F++A  LA AL+GDA++TN  +L
Sbjct: 839  NCTETPTAEFTRNPDWQFPLARMQQTVTATVGADHAWFLDAQALATALMGDALYTNMFLL 898

Query: 903  GYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEG 962
            GYAWQKG +P+SL AL RAIELNGTAV  N  A DWGR  A D   V  L     +T   
Sbjct: 899  GYAWQKGLVPVSLPALGRAIELNGTAVAANLQALDWGRRAAVDEARVRQLATPAADTP-- 956

Query: 963  AEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPL 1022
                  P    A LE+++A R + LT YQDAA A+ +R  +  +R AE+ L      LP+
Sbjct: 957  ------PPRPDAALEEVLALREQELTDYQDAALARRYRQRIEALRQAEAPL---DPALPV 1007

Query: 1023 TEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRD 1082
            T AAARN  K++A KDEYEVARL+T P F  +LR  F GEPG+DY ++  LAPPL A+ D
Sbjct: 1008 TLAAARNYFKVLAIKDEYEVARLHTRPEFFARLRQTFAGEPGKDYAVHVHLAPPLWARPD 1067

Query: 1083 EK-GHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELT 1141
             + G + KR++GP  +    +LA+LK LRG   DVFG TAERR ERAL   Y A LE + 
Sbjct: 1068 PRSGQIRKRQYGPWMLGALKLLARLKFLRGTALDVFGHTAERRMERALQAGYEADLERIL 1127

Query: 1142 RGLSAAN-HATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQ 1186
              L+A + H   + LA LP+ +RG+GHVK  +  K R +   LL +
Sbjct: 1128 EALAAGSAHPALLELARLPESVRGYGHVKAASAEKARQQRQELLRK 1173


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: 3365
Number of extensions: 135
Number of successful extensions: 8
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: 1183
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1136
Effective search space:  1306400
Effective search space used:  1306400
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 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