GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Marivita geojedonensis DPG-138

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 WP_085636091.1 MGEO_RS07450 dipeptide/oligopeptide/nickel ABC transporter permease/ATP-binding protein

Query= TCDB::Q9X271
         (324 letters)



>NCBI__GCF_002115805.1:WP_085636091.1
          Length = 628

 Score =  277 bits (708), Expect = 6e-79
 Identities = 144/314 (45%), Positives = 199/314 (63%), Gaps = 1/314 (0%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLI-NRNG 62
           LL++  L+ +F   + + +AV G+   +  GE LGI+GESGSGKSV+ LS++ L+ +  G
Sbjct: 303 LLSITALETQFRVKDRVYRAVGGVDLHVEPGECLGIIGESGSGKSVTALSIMGLVASPPG 362

Query: 63  RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122
            I  G A + G DL+    E LR++RG+ ++ IFQ+P+ +L+P+  VG Q++E +  H  
Sbjct: 363 VITGGAAYYRGDDLIGAPYEVLRSLRGRHVAYIFQDPLATLHPLYTVGDQLIEAVRAHHP 422

Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182
               EAR RAI LL+ V IP + +R  +YP + SGGMRQRV IAMALA  P ++IADEPT
Sbjct: 423 TPRAEARVRAISLLKSVRIPNAEQRIDSYPHEMSGGMRQRVGIAMALANDPDIIIADEPT 482

Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242
           TALDVT+QAQI+ LL +L+ E G+++IFITHD  V    CDR+  MYAG+IVE  P + I
Sbjct: 483 TALDVTVQAQILSLLNDLRRERGLAIIFITHDFGVVAQLCDRVAVMYAGRIVEGGPTDTI 542

Query: 243 LKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREE 302
           L  P HPYT  L+    E+G   + L  IPG PP     P+GC F  RC      C+  +
Sbjct: 543 LNAPAHPYTSRLMACVPELGQGRRVLAAIPGLPPAVDNLPTGCAFADRCHKVQPACRTAD 602

Query: 303 PPLVNISENHRVAC 316
            PL   S+ +RV C
Sbjct: 603 IPLSGPSDGNRVRC 616


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: 422
Number of extensions: 14
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: 324
Length of database: 628
Length adjustment: 33
Effective length of query: 291
Effective length of database: 595
Effective search space:   173145
Effective search space used:   173145
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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