GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Sinorhizobium meliloti 1021

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Smeli:SM_b20235
          Length = 363

 Score =  331 bits (848), Expect = 2e-95
 Identities = 194/375 (51%), Positives = 241/375 (64%), Gaps = 24/375 (6%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA V + ++ K + G  E  V   + +I D EF   VGPSGCGK+T LRMIAGLE+I++G
Sbjct: 1   MASVEIRNVVKRF-GALE-VVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            + IG   VN+V PKDR+I+MVFQNYALYPHMTV +NMAF L+L ++PK E  R+V EAA
Sbjct: 59  AVVIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAA 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
            +L +  LLDR P  LSGGQRQRVA+GRAIVR P+VFL DEPLSNLDAKLRVQMRAEI+ 
Sbjct: 119 TMLGLGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIKG 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LHQRL+TT IYVTHDQ EAMTM DRIVVMRDG ++Q  TP  ++  P+N+FVA FIGSP+
Sbjct: 179 LHQRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPS 238

Query: 241 MNFIRGEIVQDGDAFYFRAP-SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299
           MNFI GE+V       FRAP  I +  P+     L   G    P V G+RP  L      
Sbjct: 239 MNFIEGEVV----GGTFRAPGGIIIPAPD-----LAHKG----PTVAGIRPNKLQ----I 281

Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIH 359
             T P +    +V +VE  G E +L   +G   +   +  R     G  + LA     +H
Sbjct: 282 GATGPSA----KVLIVEPTGDETHLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVH 337

Query: 360 IFDAETEESIGFAAG 374
            FD +T   +G   G
Sbjct: 338 FFDGQTTLRLGALPG 352


Lambda     K      H
   0.321    0.138    0.395 

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: 436
Number of extensions: 19
Number of successful extensions: 2
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: 384
Length of database: 363
Length adjustment: 30
Effective length of query: 354
Effective length of database: 333
Effective search space:   117882
Effective search space used:   117882
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: 50 (23.9 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