GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SM_b20235 SM_b20235 sugar ABC transporter
           ATP-binding protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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