GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Cupriavidus basilensis 4G11

Align Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale)
to candidate RR42_RS21615 RR42_RS21615 alcohol dehydrogenase

Query= uniprot:A4PIB1
         (441 letters)



>FitnessBrowser__Cup4G11:RR42_RS21615
          Length = 1000

 Score =  230 bits (586), Expect = 2e-64
 Identities = 154/395 (38%), Positives = 209/395 (52%), Gaps = 21/395 (5%)

Query: 19  ICVVQSSGAYAADADLIKRGAYVAVLGDCEACHTAHDGKSLAGGLALQSPLGAIYSTNIT 78
           I  V   GA    A  I+RG  VA  GDC  CHTA +G   AGGLAL +P G IYSTNIT
Sbjct: 588 IAPVAPPGAGFYSAATIERGRLVAAAGDCAVCHTAPNGARNAGGLALDTPFGTIYSTNIT 647

Query: 79  PDRDTGIGTWSYEDFARLMRRGIRKDGSSVYPAMPYPSYSKMTDEDLQALYAYLTQGVAP 138
           PD +TGIG WSY  F R MR+GI +DG  +YPA PY +++K +D DLQALYAYL     P
Sbjct: 648 PDVETGIGNWSYAAFERAMRQGIHRDGRHLYPAFPYTAFAKTSDGDLQALYAYL-MAAEP 706

Query: 139 VSLKNRAPDIPWLLSARWPLAIWRLLFAPSPAPPLPSAPHDDTSDALVERGRYLVEGPGH 198
           V  K     + +  + R  +A W LLF  SP P       D    A   RG YL EG GH
Sbjct: 707 VRAKAPETALAFPYNLRPLMAGWNLLF-HSPKP----FEADPARSAQWNRGAYLAEGLGH 761

Query: 199 CGSCHTPRNFVLAEKVQTAADGPKYLSGGFIVDNWVAPSLRSDDAGGLVGWTPEDIVAFL 258
           C +CH+PRN + AE+      G +YL GG   + W AP+L    +   V WT + + ++L
Sbjct: 762 CSACHSPRNALGAEQ-----GGRRYLGGG-EAEGWEAPAL-GKLSHAPVPWTEQALFSYL 814

Query: 259 KTG-RNRHGATFGAMNGVITHSTSLTDDHDLAAIAAFLKTLG-PPPGVSVQAFHYDDTVS 316
           +TG    HGA  G M  VI    +L  + D+ AIA ++ + G   P  ++ +        
Sbjct: 815 RTGYAPHHGAAAGPMAPVI-EELALLPEEDVRAIAHYVASFGDAQPDAALASAQARQLEQ 873

Query: 317 RQLFAGK-MPSEGARIYVDRCAACHRTD-GHGYPGVFPPLAGNPVLQGPDATSAAHIILS 374
           R   A + +    AR+Y + CA CH++D G    G+ P LA N  L G    +   ++L 
Sbjct: 874 RSADAARTLGGPAARLYQNACAVCHQSDQGIRQFGIKPSLALNTNLHGDKPDNLIRVLLD 933

Query: 375 GGRLPGVAAAPSSLVMGSYRDVLDNQQIADLVTFL 409
           G   PG +       M ++ + LD++Q+  LV +L
Sbjct: 934 GIPTPGTSDLG---YMPAFGESLDDRQLTQLVHYL 965


Lambda     K      H
   0.318    0.135    0.420 

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: 1272
Number of extensions: 83
Number of successful extensions: 6
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: 441
Length of database: 1000
Length adjustment: 38
Effective length of query: 403
Effective length of database: 962
Effective search space:   387686
Effective search space used:   387686
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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