GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1749 in Dechlorosoma suillum PS

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Dsui_0415 Dsui_0415 oligopeptide/dipeptide ABC transporter, ATP-binding protein

Query= TCDB::Q9X271
         (324 letters)



>lcl|FitnessBrowser__PS:Dsui_0415 Dsui_0415 oligopeptide/dipeptide
           ABC transporter, ATP-binding protein
          Length = 326

 Score =  280 bits (717), Expect = 3e-80
 Identities = 145/302 (48%), Positives = 200/302 (66%), Gaps = 1/302 (0%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63
           L+++ +L V+F+       A++ +S +L +GE LG++GESGSGKSV++ +LLRL      
Sbjct: 5   LVSIQDLTVQFNGARR-ASALNQVSLELGQGEVLGLLGESGSGKSVTLRTLLRLHPERHT 63

Query: 64  IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123
              G     G+D+L L   EL   RG  +S++FQ P  + +P+  +G Q+ E +  H  +
Sbjct: 64  RTAGRIRVDGQDVLALRGRELDRYRGGTVSMVFQEPGLAFDPVYTIGQQISEAVRVHEGV 123

Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183
               A  RA+ +LERV IP++ +RF  YP + SGGMRQR MIA+ALAC PKLL+ADEPTT
Sbjct: 124 DQATAAARALAMLERVQIPQARRRFDAYPHELSGGMRQRAMIALALACKPKLLLADEPTT 183

Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243
           ALD T+Q QI+ LL+EL+ E GMSVIF+THD+  A    DRI  MYAG+IVE+ PV +++
Sbjct: 184 ALDATVQIQILLLLRELQRETGMSVIFVTHDIGAAVEVADRIAVMYAGRIVEQGPVGQLV 243

Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303
           + P HPYT+GLL +T+    RG+ L  IPG+PP+    P GC F PRCS A E C R+ P
Sbjct: 244 RQPCHPYTRGLLAATVGHEHRGRPLEAIPGSPPDLAALPPGCSFAPRCSHASERCHRDIP 303

Query: 304 PL 305
           PL
Sbjct: 304 PL 305


Lambda     K      H
   0.320    0.139    0.401 

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: 273
Number of extensions: 9
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: 324
Length of database: 326
Length adjustment: 28
Effective length of query: 296
Effective length of database: 298
Effective search space:    88208
Effective search space used:    88208
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: 48 (23.1 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