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.
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:
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