GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Shewanella loihica PV-4

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  229 bits (585), Expect = 7e-65
 Identities = 126/275 (45%), Positives = 173/275 (62%), Gaps = 6/275 (2%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80
           V D +L+I   E    +G SG GK+T LRM+AG E  TEG +Y+  + + D+PP +R I 
Sbjct: 36  VDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQDITDMPPYERPIN 95

Query: 81  MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140
           M+FQ+YAL+PHMTV QN+AFGLK  K+PKAEI++RV+E  K++ +     RKP  LSGGQ
Sbjct: 96  MMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEPYAKRKPNQLSGGQ 155

Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200
           RQRVAL R++ + P++ L+DEP+  LD KLR QM+ E+  + + +  T + VTHDQ EAM
Sbjct: 156 RQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAVGVTCVMVTHDQEEAM 215

Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDG-DAFYFRA 259
           TM +RI +M DG I Q  +P  +Y  P N  VA FIGS  +N   G+IV+D  D      
Sbjct: 216 TMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGS--VNLFEGDIVEDEVDHVVINV 273

Query: 260 PSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLH 294
            +I      G YGV  ++      V + +RPE  H
Sbjct: 274 ANIPQPFYVG-YGV--STSVDTTQVWVAIRPEKTH 305


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: 342
Number of extensions: 12
Number of successful extensions: 1
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: 378
Length adjustment: 30
Effective length of query: 354
Effective length of database: 348
Effective search space:   123192
Effective search space used:   123192
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