GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Caulobacter crescentus NA1000

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate CCNA_02410 CCNA_02410 alpha-methylacyl-CoA racemase

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



>FitnessBrowser__Caulo:CCNA_02410
          Length = 396

 Score =  176 bits (446), Expect = 1e-48
 Identities = 129/400 (32%), Positives = 192/400 (48%), Gaps = 16/400 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  LRV++L+  +A P A  ++AD GADVIKVE P  GD  R +      D  G +    
Sbjct: 2   LEGLRVVELATYIAAPGAAGVMADWGADVIKVESP-EGDPMRRFF-----DTIGSDQDAN 55

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
             +   NR K++V +D     G+  ++ L A +DI + N +   LA  GLDY++LKA+NP
Sbjct: 56  PVFELDNRGKRAVVLDIRSDLGREALKALVATADIFLTNVRSAALARAGLDYEALKAVNP 115

Query: 124 QLIYCSITGFGQTGPYAKRAGYDF-MIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182
           +LIYCS++G+G TGP A + G D        G+ ++T  P+G E   P  +   + D +T
Sbjct: 116 RLIYCSLSGYGLTGPDADKPGMDVAAFWSRAGVGAITA-PKGTE---PFPIRTGMGDHVT 171

Query: 183 GLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242
            L + +AILAA+  R   G G+ ++ +LL   V  + +     L  G      G     +
Sbjct: 172 SLATVSAILAAVHERTRTGVGRLVETSLLRTGVYAIGSDMAIQLRFGKLASTRGRREA-V 230

Query: 243 VPYQDF-PTADGDFILTVGNDG--QFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299
            P  +F  T+DG +I  +   G   + + A  AG+P+  DDPRFAT K R  +   L+ +
Sbjct: 231 QPLANFYKTSDGRWICLLPRQGSVDWPQIAAAAGRPELVDDPRFATAKARREHGQALVDI 290

Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVA 359
             +A    T       L+   +   P     ++  D Q +A G  ++ P    G     A
Sbjct: 291 FDEAFGSMTYDAAAAALDAGDITWAPYQTPRELALDAQAEAAGCFVDTPDGAGGTFKAPA 350

Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMA 399
           +P R    P   R   P LG  T  V  R LG  E  V A
Sbjct: 351 APARFPGAPNGPRGPAPKLGADTAAVF-RELGFSEDQVAA 389


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: 439
Number of extensions: 14
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: 396
Length adjustment: 31
Effective length of query: 375
Effective length of database: 365
Effective search space:   136875
Effective search space used:   136875
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