GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SM_b20820 SM_b20820 ferredoxin reductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_478
         (461 letters)



>FitnessBrowser__Smeli:SM_b20820
          Length = 409

 Score = 72.4 bits (176), Expect = 3e-17
 Identities = 77/251 (30%), Positives = 120/251 (47%), Gaps = 24/251 (9%)

Query: 66  RHHSQGSALGITVSAPSLDIGKSVEWKDGIVD----RLTTGVAALLKKHKVQVIHG-WAK 120
           R    G  + +T + P L   +    KDG+      +   G AA  ++ ++ V+ G  A+
Sbjct: 21  REKGFGGEITLTGAEPHLPYERPPLSKDGLAQASLPKFIAG-AARYEEARITVLTGVTAE 79

Query: 121 VIDG--KTVEVGD-TRIQCEHLLLATGSKSVDLPMLPVGGPIISS----TEALA---PTS 170
            ID   K V + D   +  + LLLATG++    P +P     I +     +ALA     +
Sbjct: 80  SIDRVHKAVTLSDGVSLDYDRLLLATGARPRAFPRVPENAGRIRTLRTHADALAIRGALT 139

Query: 171 VPKHLVVVGGGYIGLELGIAYRKLGAEVSVVEAQERILP-AYDGELTQPVHEALKQLGVK 229
               L V+GGG+IGLEL    RKLGAEV +VE   R+L      E+   V E  ++ GV+
Sbjct: 140 PGARLAVIGGGFIGLELAATARKLGAEVVLVEGLPRVLSRGVPEEIAVLVAERHRREGVE 199

Query: 230 LYLKHSVEGFDAQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAM-NGA 288
           +     +   D      ++     D ++++ D ++V +G  PNT+    EA  LA+ NG 
Sbjct: 200 IICGAQIAAIDGAGDGARLL--LADGVDIEADLIVVGIGAVPNTE--LAEAAGLAIENGI 255

Query: 289 AVKIDQRCQTS 299
           AV  D+R  TS
Sbjct: 256 AV--DERLCTS 264



 Score = 29.3 bits (64), Expect = 3e-04
 Identities = 26/111 (23%), Positives = 49/111 (44%), Gaps = 17/111 (15%)

Query: 174 HLVVVGGGYIGLELGIAYRK--LGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLY 231
           H+V++G G  G     A R+   G E+++  A+   LP     L++   + L Q  +  +
Sbjct: 3   HIVIIGAGECGARAAFALREKGFGGEITLTGAEPH-LPYERPPLSK---DGLAQASLPKF 58

Query: 232 LKHSVEGFDAQASTL-----------QVRDPAGDTLNLDTDRVLVAVGRKP 271
           +  +    +A+ + L                  D ++LD DR+L+A G +P
Sbjct: 59  IAGAARYEEARITVLTGVTAESIDRVHKAVTLSDGVSLDYDRLLLATGARP 109



 Score = 28.9 bits (63), Expect = 3e-04
 Identities = 31/109 (28%), Positives = 47/109 (43%), Gaps = 15/109 (13%)

Query: 4   TLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAEQFH 63
           T    L +IGGG  G   A  A +LG   +LVEG       L+ G +P +  + VAE   
Sbjct: 139 TPGARLAVIGGGFIGLELAATARKLGAEVVLVEGLP---RVLSRG-VPEEIAVLVAE--- 191

Query: 64  QTRHHSQGSALGITVSAPSLD---IGKSVEWKDGI---VDRLTTGVAAL 106
             RH  +G  +       ++D    G  +   DG+    D +  G+ A+
Sbjct: 192 --RHRREGVEIICGAQIAAIDGAGDGARLLLADGVDIEADLIVVGIGAV 238


Lambda     K      H
   0.318    0.135    0.394 

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: 409
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 461
Length of database: 409
Length adjustment: 32
Effective length of query: 429
Effective length of database: 377
Effective search space:   161733
Effective search space used:   161733
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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