GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctP in Dechlorosoma suillum PS

Align Monocarboxylate 2-oxoacid-binding periplasmic protein all3028; Extracellular solute-binding protein; Extracytoplasmic solute receptor protein all3028; TRAP transporter monocarboxylate 2-oxoacid-binding subunit P (characterized)
to candidate Dsui_2650 Dsui_2650 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component

Query= SwissProt::Q8YSQ6
         (364 letters)



>lcl|FitnessBrowser__PS:Dsui_2650 Dsui_2650 TRAP-type
           mannitol/chloroaromatic compound transport system,
           periplasmic component
          Length = 330

 Score =  361 bits (927), Expect = e-104
 Identities = 175/323 (54%), Positives = 229/323 (70%), Gaps = 8/323 (2%)

Query: 1   MKRREVLNTAAIATATTALVSCTQTNTSSVQAGLPNVRWRMTTSWPKSLGTFIGA-ETVA 59
           M+RR+ L  A  + A  A        T+    G P VRWR+ +S+PKSL T  GA E +A
Sbjct: 1   MQRRDFLLGAGASAALGAA-------TARAADGQPVVRWRLASSYPKSLDTLYGASEVLA 53

Query: 60  KRVAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALAFATSVP 119
            RVA +T GRF+I PFAAGE+VPGLQ LDAVQ  TVECGHT   +Y+GK+ A AF + +P
Sbjct: 54  NRVAALTEGRFQIRPFAAGEIVPGLQALDAVQQDTVECGHTLGSFYVGKNRAFAFDSVLP 113

Query: 120 FGLNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVSDLKGLK 179
           FGL  +QQ AW++ G GL  ++++Y ++ VINFP G+TGAQMGGWF+KE++ ++DLKGLK
Sbjct: 114 FGLTTRQQTAWMHFGNGLTLLRELYRDYGVINFPGGNTGAQMGGWFRKELQGLADLKGLK 173

Query: 180 MRIPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKAAQFYYY 239
           MRIPGLGG++M+RLG   Q +PG ++Y AL++GAIDAAEW GPYDDEKLG  K A++YY+
Sbjct: 174 MRIPGLGGEIMARLGAVPQTIPGADVYPALEKGAIDAAEWSGPYDDEKLGFFKVARYYYH 233

Query: 240 PGWWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALTRLLAGG 299
           PGWWEP   L  LVN   W +LPK YQ+ F+ A  EA+L    +YDA N  ALTRLLA G
Sbjct: 234 PGWWEPSAQLSFLVNAREWEKLPKAYQQAFEVAAAEAHLLTTAEYDAKNPPALTRLLAQG 293

Query: 300 TKLVPYSQEIMQAAQKISFDIFE 322
            KL  +  ++M+AA + +F  +E
Sbjct: 294 VKLRRFPDDVMKAAYRAAFAFYE 316


Lambda     K      H
   0.317    0.132    0.397 

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: 413
Number of extensions: 15
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: 364
Length of database: 330
Length adjustment: 29
Effective length of query: 335
Effective length of database: 301
Effective search space:   100835
Effective search space used:   100835
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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 preprint 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