GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Acidovorax sp. GW101-3H11

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ac3H11_3532 L-carnitine dehydratase/bile acid-inducible protein F

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3532
          Length = 424

 Score =  517 bits (1332), Expect = e-151
 Identities = 256/417 (61%), Positives = 317/417 (76%), Gaps = 13/417 (3%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           GAL+ ++VLDLSRVLAGPW  Q+LADLGADV+KVERPG GDDTR WGPPFLKDA G +T 
Sbjct: 9   GALAGIKVLDLSRVLAGPWCTQVLADLGADVVKVERPGVGDDTRQWGPPFLKDAEGNDTN 68

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
           +A+YY + NRNK+SVTID   P+GQ L+R++A ++DI++ENFKVGGL  YGLD++SL+A+
Sbjct: 69  QASYYTACNRNKRSVTIDMASPDGQALIRQMAQEADIVVENFKVGGLKQYGLDHESLRAL 128

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+LIYCS+TGFGQ GPYA+RAGYD M+Q + GLMS+TG+ + + G GP++VGVA+ D+ 
Sbjct: 129 NPRLIYCSVTGFGQDGPYAERAGYDLMVQAMTGLMSITGQADTEPGGGPMRVGVAVIDLF 188

Query: 182 TGLYSTAAILAALAHRDH----VGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGN 237
           TGLY++ AILAAL  RD+     G GQHIDMALLDV +A LANQA  +L TG AP R+GN
Sbjct: 189 TGLYASNAILAALHVRDNAATGTGQGQHIDMALLDVGMAVLANQASGFLATGKAPGRMGN 248

Query: 238 AHPNIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLI 297
           +HP++ PYQDFPT DG+ +L +GNDGQF++F   A QPQWA DPRFATN +RV NR  LI
Sbjct: 249 SHPSLAPYQDFPTQDGNMLLAIGNDGQFQRFCAAANQPQWASDPRFATNTLRVQNRTDLI 308

Query: 298 PLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAG---- 353
           P +   T  +TTA+W+  LE   VPCGPIN +AQ F D QVQARGLA+ LP    G    
Sbjct: 309 PAMEAVTRTRTTADWIALLEDKAVPCGPINTIAQAFDDAQVQARGLAVTLPRWKDGEAAT 368

Query: 354 -KVPQ---VASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
            KV Q   VASP+RLS TP   RNAPP LG+HT EVL   +GLD A + A R  GV+
Sbjct: 369 DKVQQITGVASPLRLSATPPVLRNAPPALGQHTDEVLAE-MGLDAARIAALRAQGVV 424


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: 581
Number of extensions: 26
Number of successful extensions: 3
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: 424
Length adjustment: 31
Effective length of query: 375
Effective length of database: 393
Effective search space:   147375
Effective search space used:   147375
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.

Links

Downloads

Related tools

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