GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofo in Paraburkholderia bryophila 376MFSha3.1

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate H281DRAFT_05847 H281DRAFT_05847 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Burk376:H281DRAFT_05847
          Length = 1199

 Score = 1805 bits (4674), Expect = 0.0
 Identities = 875/1205 (72%), Positives = 1009/1205 (83%), Gaps = 14/1205 (1%)

Query: 1    MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60
            MNAPL      ++  AL++V+L+DKYTLERGR Y+SG QALVRLPMLQ+ERDRAAGLNTA
Sbjct: 1    MNAPLDAGQRASLEAALSSVTLDDKYTLERGRAYMSGIQALVRLPMLQQERDRAAGLNTA 60

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120
            GFISGYRGSPLG LDQSLWKAKQHLA+H +VFQ G+NEDLAAT+VWGSQQVN+YP A+++
Sbjct: 61   GFISGYRGSPLGGLDQSLWKAKQHLASHQVVFQPGVNEDLAATAVWGSQQVNLYPSAKYD 120

Query: 121  GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180
            GVF MWYGKGPGVDR+ DVFKH NSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC
Sbjct: 121  GVFSMWYGKGPGVDRSGDVFKHGNSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180

Query: 181  GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240
            GLPVL+PSNVQEYLD+GLH WAMSRYSGLWV+MKCVTDVVESSASV++DPHR +I+LP+D
Sbjct: 181  GLPVLFPSNVQEYLDFGLHGWAMSRYSGLWVAMKCVTDVVESSASVDIDPHRTQIILPED 240

Query: 241  FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300
            F +P GGLNIRWPDPPL QEARLLDYKWYA LAYVRANK+DR+EIDSPHARFGIMTGGKA
Sbjct: 241  FAMPEGGLNIRWPDPPLVQEARLLDYKWYAALAYVRANKLDRVEIDSPHARFGIMTGGKA 300

Query: 301  YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360
            YLD RQAL +LGLDDETC+RIGIRLYKVGCVWPLEA GA+AFA GL EILVVEEKRQI+E
Sbjct: 301  YLDVRQALTDLGLDDETCSRIGIRLYKVGCVWPLEAQGAQAFARGLDEILVVEEKRQILE 360

Query: 361  YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420
            YA+KEELYNW D  RP+V+GKFDEKD AGGEWS+P  NWLLPAHYELSPAIIA+AIATRL
Sbjct: 361  YAIKEELYNWPDAQRPRVFGKFDEKDGAGGEWSVPMGNWLLPAHYELSPAIIAKAIATRL 420

Query: 421  DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480
            DKF+LP+DVRARIAARIAVIEAKEKA+A PRV  ERKPWFCSGCPHNTSTNVPEGSRA+A
Sbjct: 421  DKFDLPSDVRARIAARIAVIEAKEKALARPRVEVERKPWFCSGCPHNTSTNVPEGSRAMA 480

Query: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540
            GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPF  DKHVFANLGDGTYFHSGLLAIRA+
Sbjct: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFTNDKHVFANLGDGTYFHSGLLAIRAA 540

Query: 541  IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAI 600
            IA+  NITYK+LYNDAVAMTGGQP+DG L+V  + +Q+AAEGA KI +VTDEPEKYS  +
Sbjct: 541  IASKANITYKLLYNDAVAMTGGQPVDGVLTVPQITHQLAAEGATKIAIVTDEPEKYSGNV 600

Query: 601  KLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIND 660
             L  G+++HHRD+LD +QR+LRE+PG TILIYDQTCATEKRRRRKRG YPDPA+R  IN+
Sbjct: 601  GLAPGIDIHHRDQLDEVQRQLREIPGTTILIYDQTCATEKRRRRKRGAYPDPARRVVINE 660

Query: 661  AVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKK 720
            AVCEGCGDCSVKSNCLSVEPL+TE GTKRQINQS+CNKDFSCVNGFCPSFV+ EG Q++K
Sbjct: 661  AVCEGCGDCSVKSNCLSVEPLDTEYGTKRQINQSTCNKDFSCVNGFCPSFVSVEGGQLRK 720

Query: 721  PE-RHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVL 779
            P+   G+  D +P +P+P LP +  PYGVLVTGVGGTGVVTIG LLGMAAHLENKGVTVL
Sbjct: 721  PKAASGIVADAMPPVPEPTLPSIARPYGVLVTGVGGTGVVTIGALLGMAAHLENKGVTVL 780

Query: 780  DMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRT 839
            D+ GLAQKGGAV+SHVQIA +P  +HATRIAMGEA LVIGCDAIV+A D+ +S+ Q GRT
Sbjct: 781  DVTGLAQKGGAVMSHVQIANNPGDIHATRIAMGEASLVIGCDAIVTASDECVSRMQAGRT 840

Query: 840  RAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEAC-DFINASGLAVALIGDAIFTN 898
            R ++N+A TPTAE IKNP W+FPG S E DVR   G+ C D ++A+  AVAL+GDAI+TN
Sbjct: 841  RVVLNSAHTPTAELIKNPNWRFPGSSTEADVRAGAGDECVDTVDANHFAVALLGDAIYTN 900

Query: 899  PLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDP----EHVLSLTG 954
            P VLGYAWQ+GW+PL+  +L+RAIELN   VEKN+AAF+WGR  AHDP    ++  S   
Sbjct: 901  PFVLGYAWQRGWVPLTYQSLMRAIELNNVQVEKNRAAFEWGRRAAHDPVALRKYAQSQGQ 960

Query: 955  KLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALV 1014
               +     +++ L T     L+ LI  RA +L A+Q+ AYA  +R  VS+VR AESAL 
Sbjct: 961  AGASDTPSGKIISLHTPKA--LDTLIDKRATYLAAWQNDAYADRYRALVSQVRVAESALD 1018

Query: 1015 GNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLA 1074
                 LPLTE  A+NL KLMAYKDEYEVARLY+DP F++KL+  FEG    D++L+  LA
Sbjct: 1019 SIDGQLPLTETVAKNLHKLMAYKDEYEVARLYSDPAFIEKLKASFEG----DWKLHIHLA 1074

Query: 1075 PPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYR 1134
            PP+ +K+D  GHL+K+++GP       VLAK K LRG   DVFGKT ERRTERALIGEY 
Sbjct: 1075 PPMFSKKDAHGHLIKKKYGPWVFSAMHVLAKFKFLRGTALDVFGKTEERRTERALIGEYE 1134

Query: 1135 ALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPE--T 1192
            AL+ EL  GL+  N   A+ LA+LPD IRGFGH+K++NL  VR +W  LL ++R P+  T
Sbjct: 1135 ALVRELIGGLTVQNRDLAVELANLPDGIRGFGHIKENNLKGVRVKWNELLTRWRSPQAGT 1194

Query: 1193 AQRVA 1197
             Q  A
Sbjct: 1195 TQHAA 1199


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: 3626
Number of extensions: 128
Number of successful extensions: 5
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: 1199
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1152
Effective search space:  1324800
Effective search space used:  1324800
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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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