GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Sinorhizobium meliloti 1021

Align Inositol transport system ATP-binding protein (characterized)
to candidate SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__Smeli:SM_b20503
          Length = 512

 Score =  423 bits (1087), Expect = e-123
 Identities = 221/494 (44%), Positives = 331/494 (67%), Gaps = 5/494 (1%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           +LEI N+SK F  V AL  V  R+  G V AL GENGAGKSTLM +IAG+ QP  GE+ +
Sbjct: 6   VLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVLI 65

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
            G P+   +P  AQ  GIA++HQE+ L P  +IAEN+++         ++N+ ++ R   
Sbjct: 66  EGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQLERDAQ 125

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            ++ RL   +D  ++VG+L I+ +Q+VEIAKA++ D  +LI DEPT+A+TE E   LF I
Sbjct: 126 AVMNRLA-PIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLFGI 184

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           I DLK++G  I+YI+H+M EVF++ D V VFRDG Y+  +    +  D ++ +MVGRE+S
Sbjct: 185 IRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVGREIS 244

Query: 263 QLFPLRETP---IGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319
           QL+P ++     +G+ +L+VRDL  +  F+DVSF+L  GEILG+ GL+GSGRT +AE I 
Sbjct: 245 QLYPDKQPSSERLGEPILSVRDLGGER-FRDVSFELRYGEILGVGGLIGSGRTEIAEGIC 303

Query: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379
            + P + G+I L  K +R+     A + G   L+EDRK SG+F  LS+ +N+    L   
Sbjct: 304 ALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAALDLKAL 363

Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439
           T  G +  +  RAL ED+ ++L V+   ++  + +LSGGNQQK  +A+ L  +P+++++D
Sbjct: 364 TSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDPKVILMD 423

Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499
           EPTRGIDVGAK+EI+RL+  LA  G+ +++ISSELPE++G+ DRV+V+ EG + G +  +
Sbjct: 424 EPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIAGEVSGN 483

Query: 500 EATQEKVMQLASGM 513
           E T+E +M+LASG+
Sbjct: 484 EMTEEVIMRLASGI 497


Lambda     K      H
   0.320    0.136    0.381 

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: 583
Number of extensions: 21
Number of successful extensions: 7
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: 517
Length of database: 512
Length adjustment: 35
Effective length of query: 482
Effective length of database: 477
Effective search space:   229914
Effective search space used:   229914
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 (21.8 bits)
S2: 52 (24.6 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