Aligments for a candidate for ofo in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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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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, or view the source code.

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