GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrA in Cupriavidus basilensis 4G11

Align 4-hydroxybenzoyl-CoA reductase, α subunit (EC 1.3.7.9) (characterized)
to candidate RR42_RS26495 RR42_RS26495 carbon monoxide dehydrogenase

Query= metacyc::MONOMER-14376
         (794 letters)



>FitnessBrowser__Cup4G11:RR42_RS26495
          Length = 802

 Score =  280 bits (715), Expect = 3e-79
 Identities = 241/817 (29%), Positives = 355/817 (43%), Gaps = 59/817 (7%)

Query: 15  NAAPRGVGARLPLIDGVEKVTGTARYTADLPAQGALVGKLLRSPYAHAELLEVDISEALK 74
           N   +GVGAR+   +    + G  R+ AD+   G      LRSP AHA LL +      K
Sbjct: 8   NQGGQGVGARVARKEDARHLHGKGRFVADIAMPGLQEVAFLRSPMAHARLLALH-----K 62

Query: 75  LPGVRGIVTGNDCDTPYGVIPIAQNEFP---------LARGRIRYVGEPVAAVAAVDEAT 125
             G+   V G D D    +  +A + FP         LA G++R+VGEP+A   A   A 
Sbjct: 63  PQGLEHAVIGRD-DMHGALDIVADSAFPSYQPSAQPPLAAGKVRFVGEPIAMAFAPTRAQ 121

Query: 126 TDAALALIRLKVRELPAYFDAADARKAD-VVLLHDNKKGN--IEREVHNEFGDAAAGFAA 182
            +     I  ++ ELPA  D   AR+A     +H++ K N  +       F   +     
Sbjct: 122 AEDIAERIVAELDELPALTDVDGARQASGTTRVHEHWKNNHFLTLTADKNFDTLSK---T 178

Query: 183 ADLICEETFECAEVHHAMMEPNASLAAWDNERGHLTLWSVTQVPYYVHESLARCMKLDAA 242
           A ++     + A      ME  A LA WD++   L ++S TQVP+ +   L+ C+ L+  
Sbjct: 179 ASVVVSRKIDLARQCMVPMEGKAVLAYWDHQFDQLIVYSATQVPHMIRTVLSHCLGLEQE 238

Query: 243 YIRVIKPFVGGGFGHRVETLNFEIIAGLLARAARGTVRLLQTREEAFLTHRGRPQTYVRM 302
            +RVI P VGG FG++      E+    LA   R   R ++ R E         + +  +
Sbjct: 239 KVRVISPDVGGAFGYKCVLQQEELCIAWLAMTYRKPFRFIEDRREHLTAGANSREHHYEV 298

Query: 303 KLGLTRDGRMTACEAEVVQRGGAYGGYGLVTILYAGALLNGLYDLPAVKYDGYR-----V 357
                  GR+ A +A +   GGAY  +     L  G  +  L    A  +DGYR     V
Sbjct: 299 TAYADARGRLLALDARIAIDGGAYSVWPFTIGLEPGQAIGNLPGPYA--FDGYRCITECV 356

Query: 358 YTNTPPCGAMRGHGTVNIRFAFESLLDMMAAELGLDAFAVRRRNLLK---APTETINGLK 414
            TN P     RG     + FA E L+D +A E+  + + +R  NL++    P   +    
Sbjct: 357 ATNKPGFVPYRGVARTGVCFAMELLMDALAREVKREPWEIRCENLVQPESMPYVNVTNKH 416

Query: 415 VMSYGLPECLDWVEQ---ASGWRERAARLEANSDGPIRRGIGIACSHFVSGSA------- 464
                 P  +    Q    +G RER  R   N      R +G+    +   SA       
Sbjct: 417 FDGGDYPASVRKAAQMIGLAGIRER-QRQRLNDPSAGSRYLGVGFGTYTEQSAHGTSVFA 475

Query: 465 ---KPVHFTGQPHATIALRVDFDAGITILTGASDIGQGSSTIITQVVAEILGVEYRRLRL 521
               PV   G   AT+  R+  D G+ +  G    GQG  T   Q+  EILG++  R+++
Sbjct: 476 AWGTPV-IPGFDSATV--RITPDGGLEVRVGVHSHGQGMETTFAQIANEILGIDVSRVKV 532

Query: 522 IATDSALTPKDNGSYSSRVTFMVGNAAADAARNLKAVLVAAAAKRLQVAEADVDWLGEAA 581
           +  D+ +TP   G+Y+SR   M G A + A + L   L+   A  LQ  E +    G  +
Sbjct: 533 VHGDTGVTPFSTGTYASRSLVMSGGAVSRACKALVPRLLKIGAHMLQRPEGEATLAG-GS 591

Query: 582 AVVGDASRQIPFHDIVEEALVDVGMLTVKGTFTCPPEFQGGKQRGGAVGSTMGFSYAAQA 641
              GDA+  +P  +I     ++   L      T      G K        T  F+Y+  A
Sbjct: 592 VKAGDAA--VPISEIANAWYINPQRLPANVDPTGLETTMGYKPS----VDTGSFTYSTHA 645

Query: 642 VEVSVDTELGKVTVEKVWSAIDCGFAINPMSVEGQVQGAIWMGMGQAISEETVYE-NGRH 700
             V VDT+ G V +       DCG  +NPM VEGQ  G +  G+G A+ EE  Y+ NG+ 
Sbjct: 646 ALVEVDTDSGHVEILDYVVVEDCGTMVNPMVVEGQTYGGVAQGIGTAMFEEMRYDGNGQP 705

Query: 701 KAVSLLDYRVPTIIESPDIAVHIVESLDPNGPFGAKEASEGPLAGVMSAIAAAIEDATGT 760
            A +L DY +P   E P I +H  E+  P+  FGAK   EG      +AI  A+ DA G+
Sbjct: 706 LASTLADYMLPGPTEIPSIRIHHFETPSPHTEFGAKGMGEGGAIAPPAAIFNAVNDALGS 765

Query: 761 ---RIRATPFTPDRVFDALNRKPRPGAHVAAAAKGAA 794
               +  TP TP +V +AL R  +     A   + AA
Sbjct: 766 FGVELLETPLTPRKVLEALARAEQAREPQATPTREAA 802


Lambda     K      H
   0.319    0.135    0.397 

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: 1464
Number of extensions: 83
Number of successful extensions: 9
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: 794
Length of database: 802
Length adjustment: 41
Effective length of query: 753
Effective length of database: 761
Effective search space:   573033
Effective search space used:   573033
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: 55 (25.8 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