GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Shewanella oneidensis MR-1

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 200964 SO1802 peptide ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__MR1:200964
          Length = 335

 Score =  162 bits (411), Expect = 8e-45
 Identities = 100/310 (32%), Positives = 171/310 (55%), Gaps = 16/310 (5%)

Query: 24  PQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD----GGKIFFEGK 79
           P GK  ++A++ +S+ +  GE  GLVGESG G+S L R IL +  P+      ++ ++G 
Sbjct: 16  PHGK--VRALEKVSLTLNAGEIHGLVGESGSGRSLLARAILGIPGPNWTITADRMMWDGN 73

Query: 80  DITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRV-- 136
           ++  ++ KE +      M +IFQDP GSL+P  TVG  +   +  +      ++ K    
Sbjct: 74  NLMAMSSKERRNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMPKNPKAYFWQKHKHAKL 133

Query: 137 --EELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQ 192
             ++ L  VGI   ++ ++S+  E S G+ Q++ IA A+A  P+ ++ DEP +++++S Q
Sbjct: 134 TAQKWLHKVGIKNPQKVMSSYAWELSEGECQKVMIAMAIANQPRLLIADEPTNSMELSTQ 193

Query: 193 AQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPY 252
           AQI  LL ++ Q   +S L I+H L  +      ++V+Y G+++E G  D++   P HPY
Sbjct: 194 AQIFRLLSQLNQLQNVSILIISHELETLAQWCDHLSVLYCGQVMESGPTDELINQPYHPY 253

Query: 253 TRALLKSVPKIPW-DGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTE 311
           T+ALL ++P     +  K    +L G  P+   LP GCR   RC E +  C   +P L+ 
Sbjct: 254 TKALLDNMPDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLGPRCPEAQKKCV-NQPSLSH 312

Query: 312 VEKNHFVSCH 321
             ++ + +CH
Sbjct: 313 -SRDRYFACH 321


Lambda     K      H
   0.321    0.142    0.417 

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: 267
Number of extensions: 15
Number of successful extensions: 4
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: 328
Length of database: 335
Length adjustment: 28
Effective length of query: 300
Effective length of database: 307
Effective search space:    92100
Effective search space used:    92100
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: 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:

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