GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05847 H281DRAFT_05847
            indolepyruvate ferredoxin oxidoreductase
          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 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