GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofo in Rhodococcus qingshengii djl-6-2

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 WP_076948421.1 C1M55_RS23815 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_002893965.1:WP_076948421.1
          Length = 1151

 Score =  825 bits (2132), Expect = 0.0
 Identities = 488/1140 (42%), Positives = 664/1140 (58%), Gaps = 47/1140 (4%)

Query: 8    LDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWEA 67
            LDD+ R  +G + LTG QA+ R  + QH RD   G     F+SGY+GSPLGG+DK L   
Sbjct: 16   LDDRCRSGSGPVLLTGVQAIARGFVEQHVRDIRAGKRIATFVSGYQGSPLGGVDKMLHGM 75

Query: 68   RDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPG-AKYDGVFAMWYGKGPGVDRAGDVF 126
               L +H I F PG NEELAATAVWGSQ T+L  G A +DGV  +WYGKGPGVDRA D  
Sbjct: 76   PKVLAEHDITFIPGFNEELAATAVWGSQ-TDLPAGTATHDGVTGVWYGKGPGVDRATDTI 134

Query: 127  KHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIG 186
            +HAN  GV+P+GGV+LL GDD   KSST+P  SE +  A  +PVL P N +EI+  G+  
Sbjct: 135  RHANMYGVNPKGGVVLLVGDDPASKSSTVPAVSERSLAAMGVPVLFPRNAEEIITMGMHA 194

Query: 187  WELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPE-DFE-LPEDGVHIRWPDPPLA 244
              LSR SGC VALK +A+  D +  ++         +PE  FE  P      +   PP +
Sbjct: 195  VALSRVSGCVVALKIVADVADGAWTIDGSIADFDIVVPEVQFEGKPFVYKQRQMAAPPDS 254

Query: 245  QEKRLNLY--KIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEA 302
                 +LY  +     A+  ANNL+ + ++    ++GI  TG ++  VRQAL DLG+D+A
Sbjct: 255  VIAEADLYGPRWDLVHAYGTANNLDVIEVNPSGAKIGIAATGTTFDSVRQALADLGVDDA 314

Query: 303  LCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRP 362
                 G+R+L++GM +P+    + EFA+GL++I+VVE+K + IE Q+   LY       P
Sbjct: 315  ALHRAGIRLLRIGMCYPVVGEKIKEFAEGLEQIVVVEDKTAFIEAQIREVLYG--TDDAP 372

Query: 363  RVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARS 422
            R++G+ D QG  L+P   ELT   +   + + L P          +         L+   
Sbjct: 373  RIIGKRDGQGRLLMPASGELTAGRLLAPLRRVLKP---------HVELKRTLPAPLSLNV 423

Query: 423  YSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTET---FTQMGGEGVNW 479
             S  RT ++CSGCPHN ST +PEGS    GIGCH +V    R        TQMGGEG  W
Sbjct: 424  LSAKRTAYFCSGCPHNRSTAIPEGSIGGGGIGCHTLVTMSGREDSAVTGLTQMGGEGSQW 483

Query: 480  IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539
            IGQAPFTD PH+FQN+GDGT+FHSG LAV+A +AAGVN+TYK+LYN+ VAMTG Q  +G 
Sbjct: 484  IGQAPFTDVPHLFQNIGDGTFFHSGQLAVQACIAAGVNITYKLLYNEVVAMTGAQDAEGA 543

Query: 540  LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599
            L V QLS ++  EGVK+I + +DEP ++  R   A  T   HR  LD  Q+ELRE KGV+
Sbjct: 544  LSVAQLSHKLTTEGVKQIIICADEPSRHNKR-ALAKGTKLWHRDRLDEAQKELREIKGVT 602

Query: 600  VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659
            V+IYDQ CA + RR+RKRG +     R  IN AVCEGCGDCG KSNCL+V P++TE GRK
Sbjct: 603  VLIYDQHCAADARRQRKRGTLPTRNTRVVINEAVCEGCGDCGVKSNCLSVQPVDTEYGRK 662

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVH-GGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNV 718
             +IDQ +CN D++C++G CPSFVTV    G + P+A         + +P    L    NV
Sbjct: 663  TKIDQTSCNTDYTCMDGDCPSFVTVELVPGKKAPKAARP--VPPVVADPDFGPLTSTQNV 720

Query: 719  LIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVR 778
             + G+GG+G+ T+  +L  AA   G     LDQ GL+QK GPV +H+R ++   +  + R
Sbjct: 721  FLAGIGGTGIVTVNQVLATAALRAGLEVESLDQIGLSQKAGPVVSHLRFSSSALE-PSNR 779

Query: 779  IAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQ 838
            +  G AD ++  DL+ A  +++L   N + + ++ ++ ++ T +   +   + P      
Sbjct: 780  LTPGSADCIVAFDLLTATDNKNLDYGNAEKTVSIASTSQTPTGDMVYDKAVRYPEETSLL 839

Query: 839  AISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGV 898
            A  D V      F DA   A  L G++ A N  L+G AYQ G L + AEAIE+AI +NGV
Sbjct: 840  ARLDKVSRTLRSF-DALAAAQELFGNTAAANFLLIGAAYQSGGLRLPAEAIEEAIGINGV 898

Query: 899  SAKLNLQAFRWGRRAVLEREAVEQLARPVDMV-EPIC-------------KTLEEIVDWR 944
            +   N+ AFRWGR A+ +  A   +  P   V EP+              +TL  +V+ R
Sbjct: 899  AVDANIAAFRWGRAAIADTAAFSAVTTPAKSVREPVVAPAHMFAGTTFTGETL-RLVELR 957

Query: 945  VDFLTRYQSAGLARRYRQLVERVRDADSA--DDLALSKAVARYYFKLLAYKDEYEVARLY 1002
               L  +QS  +A+RY   V+ V  A+ A  +    S+AVAR  FK  AYKDEYEVAR+ 
Sbjct: 958  AAQLIEFQSVKIAQRYIDQVQAVWTAERAATERTDFSEAVARGLFKFTAYKDEYEVARML 1017

Query: 1003 SEPEFRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFL 1062
             +P F + +++Q      L + L P  L     V G  +K  LGP       VLAK + L
Sbjct: 1018 VDPAFIEDVKSQVPAGENLTYKLHPPILR----VMGRKKKIGLGPKSHVALKVLAKGKKL 1073

Query: 1063 RGTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVK 1122
            RGT LDPFGY H R+VER+L++EYE  + +L   L    Y  AV IAALP+ +RGY  +K
Sbjct: 1074 RGTKLDPFGYMHVRKVERELLAEYEAMIADLSRTLATDGYDRAVEIAALPDVVRGYEDIK 1133


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: 2853
Number of extensions: 136
Number of successful extensions: 11
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: 1151
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1104
Effective search space:  1224336
Effective search space used:  1224336
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 24 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