GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacE in Cupriavidus basilensis 4G11

Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate RR42_RS23085 RR42_RS23085 cytochrome C biogenesis protein CcdA

Query= reanno::BFirm:BPHYT_RS22715
         (310 letters)



>FitnessBrowser__Cup4G11:RR42_RS23085
          Length = 308

 Score =  505 bits (1300), Expect = e-148
 Identities = 253/302 (83%), Positives = 271/302 (89%)

Query: 9   AMRGVFPVAPTIFDDAGRLDLEGQKRCIDFMIDAGSNGLCILANFSEQFALSDDERNTLM 68
           A RGVFPVAPTIFD+ G LDL+GQ+RCIDFMIDAGSNG+CILANFSEQF L+DDER+ LM
Sbjct: 7   AYRGVFPVAPTIFDEQGGLDLDGQRRCIDFMIDAGSNGICILANFSEQFVLADDERSLLM 66

Query: 69  HVVLEHVAGRVPVIVTTTHFSSYQCAERSRSAQAAGAAMVMVMPPYHGATIRIGERGIYE 128
             VLEHVAGRVPVIVTTTHFSS  CAERSR+AQ AGAAMVMVMPPYHGATIR+ ER IYE
Sbjct: 67  TTVLEHVAGRVPVIVTTTHFSSRICAERSRAAQDAGAAMVMVMPPYHGATIRVPERAIYE 126

Query: 129 FYRTVSDAIGIPIMIQDAPVSGTPLSAPFLARMAREIDNVSYFKIEVPQAANKLRELIEL 188
           F+ TVS AI IPIMIQDAPVSGT LSAPFLARMA+EI NVSYFKIEVPQAA KLRELI L
Sbjct: 127 FFATVSAAIDIPIMIQDAPVSGTTLSAPFLARMAKEIANVSYFKIEVPQAAVKLRELIAL 186

Query: 189 GGDAIVGPWDGEEAITLMADLDAGATGSMTGGGYADGIRLIVDAYAAGDTEAAAAHYQQW 248
           GGDAIVGPWDGEEAITLMADLDAGATG+MTG G+ DGIR IVDAY AGDTE AA HYQQW
Sbjct: 187 GGDAIVGPWDGEEAITLMADLDAGATGAMTGAGFPDGIRKIVDAYQAGDTELAAQHYQQW 246

Query: 249 LPLINYENRQGGLASCKALMKEGGVIRSDAVRHPLPQMHPATREGLLKVARRLDPLVLRW 308
           LPLINYENRQG LA+ KALMKEGGVI SDA+RHPL  MHPATR GLL++ARRLDP+VLRW
Sbjct: 247 LPLINYENRQGWLATAKALMKEGGVIASDALRHPLQPMHPATRAGLLQIARRLDPMVLRW 306

Query: 309 GR 310
           G+
Sbjct: 307 GK 308


Lambda     K      H
   0.321    0.136    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: 359
Number of extensions: 6
Number of successful extensions: 1
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: 310
Length of database: 308
Length adjustment: 27
Effective length of query: 283
Effective length of database: 281
Effective search space:    79523
Effective search space used:    79523
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 (21.9 bits)
S2: 48 (23.1 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