GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofo in Phaeobacter inhibens BS107

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate GFF1685 PGA1_c17080 pyruvate ferredoxin/flavodoxin oxidoreductase-like protein

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



>FitnessBrowser__Phaeo:GFF1685
          Length = 1139

 Score = 1031 bits (2665), Expect = 0.0
 Identities = 557/1178 (47%), Positives = 758/1178 (64%), Gaps = 46/1178 (3%)

Query: 20   VSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLW 79
            +SL DK+ L + +V ++GTQALVRL ++Q+ RD+AAGLNTAG ++GYRGSPLGA+D  + 
Sbjct: 6    ISLNDKFDLTKSQVMLNGTQALVRLMLMQKHRDKAAGLNTAGLVTGYRGSPLGAVDMQMK 65

Query: 80   KAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDV 139
            +A++HL A D+ FQ GLNEDLA T++WG+QQ  +  + +++GVFG+WYGKGPGVDR+ D 
Sbjct: 66   RAEKHLTASDVTFQFGLNEDLAVTALWGAQQAEVRGEGKYDGVFGLWYGKGPGVDRSGDA 125

Query: 140  FKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLH 199
             +HAN AGSS+HGGVLV  GDDH  +SST+ HQSE     C LP++ P+ VQE LDYG +
Sbjct: 126  IRHANMAGSSKHGGVLVAMGDDHTGESSTVLHQSEWSLMDCYLPIVSPAGVQEILDYGAY 185

Query: 200  AWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQ 259
              A+SR+SGLWV +K + D +E ++ V+ DP R+++V P +F +P  GLNIR  D    Q
Sbjct: 186  GLALSRFSGLWVGLKTMKDTIEVTSVVDGDPDRMKLVTP-EFDMPADGLNIRLDDDRFRQ 244

Query: 260  EARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCA 319
            E R++DYK +A  A+  ANK+D+     P A+ G +  GK +LD   A++ L +D+    
Sbjct: 245  ENRIIDYKRFAAEAFSHANKMDKRMWGKPGAKIGFVAAGKNWLDLVHAMSLLNIDETMAE 304

Query: 320  RIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVY 379
            R+GI  YKVG  WPL+  G   +AEGL  I+VVEEKR+++E  +KE +++ R   R  VY
Sbjct: 305  RLGITTYKVGQTWPLDMKGFNDWAEGLDLIVVVEEKRKLIEIQIKEAIFDDRQGRR--VY 362

Query: 380  GKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAARIAV 439
            G +      GG  ++ +   L P  Y L P +IA  +   L   E   +  A I A +  
Sbjct: 363  GWY-----KGGAGAMHREE-LFPTKYALDPIMIAEKLGQIL--IEEGRETEA-IRAGLTA 413

Query: 440  IEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTSTFS 499
            ++  ++A     +AA R P+FCSGCPHN+ST +P+GSRA AGIGCH+M  WMDR T+ F+
Sbjct: 414  LDDAKRADNAEEIAA-RLPYFCSGCPHNSSTKLPDGSRAYAGIGCHFMVQWMDRETTGFT 472

Query: 500  QMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAVAM 559
             MGGEGV W+G+APF+  KHVF NLGDGTY HSG+ AIRA++A G NIT+KILYNDAVAM
Sbjct: 473  HMGGEGVNWVGEAPFSNRKHVFQNLGDGTYNHSGVQAIRAALAEGTNITFKILYNDAVAM 532

Query: 560  TGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRIQR 619
            TGGQ  +G L+   +A+++ A G + I VV DE E   A +  P G+ +H R EL  +Q+
Sbjct: 533  TGGQEAEGGLTAHQIAHELTAMGMKTIAVVYDEKEDVDAKL-FPAGMRMHERAELMAVQK 591

Query: 620  ELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSVE 679
            E+  V G + +IY QTCA EKRRRRK+G +PDP +R FIN  VCEGCGDC V+SNC+S+ 
Sbjct: 592  EMETVEGVSAIIYIQTCAAEKRRRRKKGLFPDPDQRVFINSDVCEGCGDCGVQSNCVSIV 651

Query: 680  PLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQPAL 739
            P ETELG KR I+QSSCNKDFSCV GFCPSF+T EGA+++K     +   +LP LP+P L
Sbjct: 652  PKETELGRKRAIDQSSCNKDFSCVKGFCPSFLTIEGAKIRKEPTAAL---DLPDLPKPEL 708

Query: 740  PGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIAA 799
            P +   + V++TGVGGTGVVTIG +L  AA ++ KG  +++MAGLAQKGGAV  H +IA 
Sbjct: 709  PSINGTHNVVITGVGGTGVVTIGAVLAQAAQIDGKGAGMMEMAGLAQKGGAVHIHCRIAN 768

Query: 800  HPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPKW 859
             P+ + A R+A GEA  +IG D +VSA    I   + G+T A+VN+ +  T +F ++  +
Sbjct: 769  KPEDISAIRVATGEAHALIGGDLVVSAGAKTIGLMKTGKTGAVVNSHEIITGDFTRDTDF 828

Query: 860  QFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDALV 919
            Q P    +  +   + +  D  +AS LA A +GD+IF+N ++ G AWQ+G LP+SL+A+ 
Sbjct: 829  QLPTDRLQVALEARLRDRLDLFDASDLARASMGDSIFSNMMIFGAAWQRGLLPISLEAIQ 888

Query: 920  RAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGALLEKL 979
             AI LNG AVE+N  AFD GR     P+ V  L            VV+LP S    LE+ 
Sbjct: 889  EAITLNGAAVERNLRAFDIGRWAVLYPQEVQKLI--------APNVVELPKS----LEEQ 936

Query: 980  IAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKDE 1039
            IA R+  L  YQ    A+ +   +  +  A+ A         L E+ A+   KL++YKDE
Sbjct: 937  IAFRSAQLVDYQGPRLAKRYGKMLDGI--ADKA---------LKESVAKGYHKLLSYKDE 985

Query: 1040 YEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKL 1099
            YEVARL       +K   +FEG    D ++++ LAPP++  +D  G   KR+FGP   + 
Sbjct: 986  YEVARLLLSS--REKAEAEFEG----DLKISYNLAPPMLTGKDPDGRPKKRKFGPGLERG 1039

Query: 1100 FGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAITLASLP 1159
              +LAK KGLRG   DVFG TAER+ ERALI +Y A ++E     S    A  I LA LP
Sbjct: 1040 LRLLAKFKGLRGTPLDVFGYTAERKMERALIAQYEADMKEWLPKASPEIMAPLIALAELP 1099

Query: 1160 DDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQRVA 1197
             +IRGFG VK  N +K   R   LL   RH  T  + A
Sbjct: 1100 LEIRGFGPVKQANESKAAKRREELLAALRHGGTELKTA 1137


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: 3144
Number of extensions: 152
Number of successful extensions: 7
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: 1139
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1092
Effective search space:  1255800
Effective search space used:  1255800
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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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:

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:

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:

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:

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