GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofo in Phaeobacter inhibens BS107

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate GFF438 PGA1_c04490 indolepyruvate oxidoreductase

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>FitnessBrowser__Phaeo:GFF438
          Length = 1140

 Score = 1036 bits (2679), Expect = 0.0
 Identities = 542/1137 (47%), Positives = 737/1137 (64%), Gaps = 11/1137 (0%)

Query: 7    RLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWE 66
            +LDD+Y    G ++LTGTQAL R+ + Q +RD++ GLNT GF+SGYRGSPLGG+D   W 
Sbjct: 12   QLDDRYDYTKGRVFLTGTQALARVMLDQARRDRSAGLNTAGFVSGYRGSPLGGVDLEFWR 71

Query: 67   ARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDVF 126
            +R  +  H I F P VNE+L ATAV G+QQ  L P  + +GVF+MWYGKGPGVDR+GD  
Sbjct: 72   SRKRMDAHNITFMPAVNEDLGATAVLGAQQAILDPHCEVEGVFSMWYGKGPGVDRSGDAL 131

Query: 127  KHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIG 186
            KH NA G S +GGVL++AGDDHGC SS++PHQS+ AF++  +PVLNPA+V E L +G  G
Sbjct: 132  KHGNAYGSSEKGGVLVVAGDDHGCVSSSMPHQSDVAFMSWFMPVLNPADVSEFLQFGEYG 191

Query: 187  WELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPLAQE 246
            + LSRYSG WV  K ++E V+S+  VE+ P R  T  PE  + P  G+HIR  D P  + 
Sbjct: 192  FALSRYSGTWVGFKAVSETVESARSVELRPDRSFT-YPELPDYP-GGLHIRRSDLPSPEI 249

Query: 247  KRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALCAS 306
            +     K+ A RAFA AN ++  + D P  + G +TTGK +LD+ +AL  LGLD+A C  
Sbjct: 250  ETRIHAKLRAVRAFAEANPIDTRIYDLPKAKFGFVTTGKGHLDLMEALRLLGLDQAACKR 309

Query: 307  VGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRVVG 366
            +G+ + KVGM WPL       F +G  E+LVVEEKR IIE Q     Y+WP  K  R+VG
Sbjct: 310  LGIDIYKVGMVWPLARTEALRFVKGKQEVLVVEEKRGIIESQFKEYFYDWPGDKPERMVG 369

Query: 367  EFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYSTV 426
            + D QGN L+P   EL+P  +  ++A+RL   +  +++  R   L A+   L     +T 
Sbjct: 370  KHDSQGNPLIPWTGELSPLTLVPIVAERLNRFFPEENLLDRANALTAQPPRLLNVPGAT- 428

Query: 427  RTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQAPFT 486
            RTP++CSGCPHN+STK+PEGS+A++GIGCH M  WMDR T  + QMGGEGV W   + F 
Sbjct: 429  RTPYFCSGCPHNTSTKLPEGSKANSGIGCHVMASWMDRDTAGYAQMGGEGVPWTVASKFN 488

Query: 487  DTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQLS 546
               H+FQNLG+GT++HSGSLA+R AVAA  N+TYKILYNDAVAMTGGQP+DG + V  ++
Sbjct: 489  GGKHVFQNLGEGTWYHSGSLAIRQAVAADTNITYKILYNDAVAMTGGQPVDGPVSVSGIA 548

Query: 547  RQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIYDQT 606
            +    EGV RIALVSD+ +K+ S+  F   TSFH R +LD+VQRELRE  GV+V+IY+QT
Sbjct: 549  QTCRAEGVDRIALVSDDIEKF-SKSEFPAGTSFHDRSDLDSVQRELREIPGVTVLIYEQT 607

Query: 607  CATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREIDQNA 666
            CATEKRRRRKRG MEDP + AFIN   CEGCGDC  +SNCL+V P ET  GRKR+I+ ++
Sbjct: 608  CATEKRRRRKRGTMEDPKRFAFINDLACEGCGDCSVESNCLSVEPKETPFGRKRKINLSS 667

Query: 667  CNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAAT--LPEPQHPTLDRPWNVLIPGVG 724
            CNKDFSC+ GFCPSFVTV G   RK E  A    A T  LP P  P+L  P+++L+ GVG
Sbjct: 668  CNKDFSCLNGFCPSFVTVEGATRRKKEVAALDASALTADLPSPALPSLKEPFDLLVTGVG 727

Query: 725  GSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIAAGEA 784
            G+GV T+GAL+ MAAHLEGKG +VLD  G AQKFG V  ++R++     ++ VRI    A
Sbjct: 728  GTGVVTVGALITMAAHLEGKGASVLDFTGFAQKFGTVLGYIRLSNTPEALHQVRIDQSAA 787

Query: 785  DLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAISDAV 844
            D ++GCD++V++  ++     +  +  V+N  E  T +     DA +       +I+D +
Sbjct: 788  DAVIGCDVVVSSAPKASAHYRDG-TKMVLNRAEMPTGDLVLRRDADLMANLRETSIADVI 846

Query: 845  GADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSAKLNL 904
            GAD     +A   A  LLGD++  N+ +LGFA+Q GL+P+S  A+++AI LNGV+ + N 
Sbjct: 847  GADNLSGFNANEAAETLLGDAVLANVMMLGFAWQNGLVPVSLGALDQAIVLNGVAIEKNR 906

Query: 905  QAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRYRQLV 964
             AF  GR    +   +  L    D  E   +TL E++D R  FLT YQ    A+ Y  L+
Sbjct: 907  LAFAIGRAFAHDPARLSDLYHEADAPE---ETLAELIDRRATFLTGYQDVAYAQSYTALL 963

Query: 965  ERVRDA-DSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYKLQF 1023
            E +R+A  S    AL  A AR  FKL+AYKDE+EVARL S+  F+ QLEA+F+GD+++ +
Sbjct: 964  EVLRNALPSKGSDALVTAAARSLFKLMAYKDEFEVARLLSDDSFKHQLEAEFDGDFRVNY 1023

Query: 1024 HLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVERQLI 1083
            HLAP  L+++    G P+K + G W+     +LAK R +RG+  +PFG   + R+ R L+
Sbjct: 1024 HLAPPLLSRKSDARGRPQKMQFGAWMRPALRLLAKGRRMRGSRWNPFGRHEEARLHRDLL 1083

Query: 1084 SEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQL 1140
            + Y+  +          ++   + + + P  IRGYGPV+  +  K + +     E L
Sbjct: 1084 AWYQTIITRTAEHYSHEHHDGWLKVLSAPMDIRGYGPVRMAAAEKVKAEVSARLETL 1140


Lambda     K      H
   0.319    0.136    0.405 

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: 2932
Number of extensions: 119
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: 1156
Length of database: 1140
Length adjustment: 46
Effective length of query: 1110
Effective length of database: 1094
Effective search space:  1214340
Effective search space used:  1214340
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 (21.8 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