GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaD in Sinorhizobium meliloti 1021

Align D-lysine oxidase (EC 1.4.3.3) (characterized)
to candidate SMc00797 SMc00797 oxidoreductase

Query= metacyc::G1G01-3833-MONOMER
         (414 letters)



>FitnessBrowser__Smeli:SMc00797
          Length = 417

 Score =  385 bits (989), Expect = e-111
 Identities = 197/416 (47%), Positives = 252/416 (60%), Gaps = 4/416 (0%)

Query: 1   MHCQTLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPR 60
           M    +VLGAGIVG+S+A+HL   G+ V+L+DR   G  TS+GNAGLI+R  V PY FP 
Sbjct: 1   MKTDVVVLGAGIVGISSAIHLARLGKSVVLLDRRGAGEETSYGNAGLIQREGVFPYGFPH 60

Query: 61  QLSALLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEH 120
              AL RY LN   D  Y    LP   P+L RYW  S   +    A    PL++  + EH
Sbjct: 61  NFGALFRYALNNTIDASYHFRALPSLVPFLARYWWHSGFTQHQKIAHLYAPLIEHSIAEH 120

Query: 121 DALIAAAGLEGLVQAKGWIEVFRDPALFEQAKTDAKGLSR-YGLRFEILECGQLQAREHQ 179
             LI A+G   L++  GW++VFR     + A  DA+ LS  +G+  + L   +L+  E  
Sbjct: 121 QDLIDASGAGDLIRKDGWMKVFRTEKERDAAYKDAERLSAGFGVNHQKLSTSELKTIEPS 180

Query: 180 LDATVVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQA--NGQWRVESR 237
           + A + GG+ W DP ++ +P +L + Y A F   GG+ V GDA +L        WRV + 
Sbjct: 181 IQAELAGGLRWTDPWSIRDPHSLNKAYLAYFQSLGGRLVSGDAATLEHILEGAGWRVATP 240

Query: 238 RGPITADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYV 297
            GP+ A EVV  LGP +  +   LGY  PLA+KRGYHMHY  R+GAQL + + D + GY 
Sbjct: 241 DGPLEAREVVVALGPWADTVTRKLGYHFPLAVKRGYHMHYGIREGAQLNNWVLDAEKGYF 300

Query: 298 LAPMARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPD 357
           LAPM RG+RLTTG EF    AP   +QL R E +AR+ FP L +R D+ PW+G RPC PD
Sbjct: 301 LAPMLRGIRLTTGAEFALRDAPKTPVQLTRAERVAREFFP-LAERRDEEPWMGARPCTPD 359

Query: 358 MRPVIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRF 413
           M PVIG APRH GLWF FGHAHHG+TLGPV GR LA+ +TGE P  D  PY   RF
Sbjct: 360 MMPVIGKAPRHEGLWFAFGHAHHGMTLGPVTGRALAQAMTGEKPVIDITPYRPERF 415


Lambda     K      H
   0.322    0.140    0.447 

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: 553
Number of extensions: 30
Number of successful extensions: 5
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: 414
Length of database: 417
Length adjustment: 31
Effective length of query: 383
Effective length of database: 386
Effective search space:   147838
Effective search space used:   147838
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: 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