Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Pf6N2E2_5708 Alpha-methylacyl-CoA racemase (EC 5.1.99.4)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5708 Length = 393 Score = 192 bits (487), Expect = 2e-53 Identities = 138/408 (33%), Positives = 202/408 (49%), Gaps = 21/408 (5%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L+ L+VLD S +L GP+A +LAD+GA+V+++E P D R P + Sbjct: 3 GPLASLKVLDFSTLLPGPFASLLLADMGAEVLRIESPTRQDLLRVLPP--------HDQG 54 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 +A + NRNK+S+ +D +PE +V +L DIL+E F+ G + GL Y++LKAI Sbjct: 55 SSASHAYLNRNKRSLALDLKQPEALAVVTQLLEDYDILLEQFRPGVMERLGLGYEALKAI 114 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP+LIY SITG+GQTGPY RAG+D L GL S TGR + +GP+ +G+ DI Sbjct: 115 NPRLIYVSITGYGQTGPYKDRAGHDINYLALAGLASHTGRAD----SGPLPLGIQAADIA 170 Query: 182 TG-LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 G L+ +LAA+ R G GQH+D+++ D + A YL G P+R Sbjct: 171 GGSLHGVIGLLAAVIARQQTGQGQHLDVSMTDCVFSLNAMAGAGYLACGVEPEREKQMLN 230 Query: 241 NIVPYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299 Y + T D ++ + F + E G+P+ A + + A + L Sbjct: 231 GGSFYDYYRTRDARWMSVGSLEPVFMQALCEALGRPELAAQGLSPKPEQQHALKQAL--- 287 Query: 300 IRQATVFKTT-AEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQV 358 QA K AE + P+ L + PQ+QAR L ++P Q+ Sbjct: 288 --QAEFEKRDFAELCSLFAGIDACVEPVLSLEEAVRHPQLQARELVTQVPRGDGSSQAQM 345 Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 A P+R SE E R+ LG HT +VL LG + R+A V+ Sbjct: 346 ACPLRFSEGLPEPRHIGAGLGAHTDQVLGE-LGFSAQRIAQLRDAKVI 392 Lambda K H 0.319 0.137 0.408 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: 431 Number of extensions: 14 Number of successful extensions: 4 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: 406 Length of database: 393 Length adjustment: 31 Effective length of query: 375 Effective length of database: 362 Effective search space: 135750 Effective search space used: 135750 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 (21.7 bits) S2: 50 (23.9 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