GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupB in Dinoroseobacter shibae DFL-12

Align Purine/cytidine ABC transporter permease protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate 3609460 Dshi_2844 inner-membrane translocator (RefSeq)

Query= TCDB::A2RKA6
         (364 letters)



>lcl|FitnessBrowser__Dino:3609460 Dshi_2844 inner-membrane
           translocator (RefSeq)
          Length = 372

 Score =  170 bits (430), Expect = 6e-47
 Identities = 115/363 (31%), Positives = 191/363 (52%), Gaps = 8/363 (2%)

Query: 8   VLVPLIAIVFGFLLGAIIMLAFGYNPIWGYEDLFISALGSARSIGETLQTMGPLILTALS 67
           +LVPL++++  F++  ++++A G NP    + +   ALGS    G TL      I T L+
Sbjct: 11  LLVPLLSVLIAFVISGLVIIAIGENPWEALKLMVTGALGSTYGWGYTLYYATNFIFTGLA 70

Query: 68  FAVAMKVGLFNIGMSGQALAGWISSMWFALSFPDIPRLLMIPLVVIIGMVFGAFMGFIPG 127
            AVA    +FNIG  GQA+ G +      L  P     + +P  VI G VFGA    IP 
Sbjct: 71  VAVAFHARMFNIGGEGQAMLGGLGVALICLYIPWPHWAMALPAAVIGGAVFGAAWAAIPA 130

Query: 128 ILRALLGTSEVITTIMLNYIMLFFSTFMIHSMFQKNILMDNTT----DQTKLISANASFR 183
            L+A  G+  VITTIM N+I      +++ +  +    MD +T    + T L + +    
Sbjct: 131 YLQAKRGSHIVITTIMFNFIGAAVLNYLLVNQLRPQGSMDPSTAKFPEATHLPTLHDLLA 190

Query: 184 TNWMSSLTDNSTLNIGLIIAIIALVIMAIIFTKTTLGFEIKAVGLNPDASEYAGISAKRT 243
              +   +  + +NI L++A++A  +  ++  +T LG+EI+A G +  A+ YAGIS  + 
Sbjct: 191 PLGI-EFSRAAPVNISLLVALVACYLFWLLIWRTKLGYEIRAYGNSETAAVYAGISPTKI 249

Query: 244 LILSMVVAGALAGLGGVVYGFGYMQNFVSQSASLDIGFYGMAVALLGGNSPIGILFAALL 303
           ++++M+++G LAG+  +    G  +  V  +     GF G+AVAL+G + P+G+L AA+L
Sbjct: 250 IMVAMLISGGLAGMMAINNVMGEAERLVLNAVE-GAGFIGIAVALMGRSHPVGVLLAAIL 308

Query: 304 FSVL-QTGAPGMTNDGIPPEIVKVVTAAIIFFI-AVKFIIEVMLPKAKAIKASEATKKKG 361
           F  L Q GA       IP E++ V+ A +I F  A+  ++ + + KA        T ++ 
Sbjct: 309 FGFLYQGGAELALWTNIPRELIVVIQALVILFTGALDNMVRMPIEKAFLAAHRRKTARRS 368

Query: 362 EKA 364
           E A
Sbjct: 369 EPA 371


Lambda     K      H
   0.327    0.141    0.404 

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: 302
Number of extensions: 13
Number of successful extensions: 3
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: 364
Length of database: 372
Length adjustment: 30
Effective length of query: 334
Effective length of database: 342
Effective search space:   114228
Effective search space used:   114228
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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