GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacIICB in Tatumella morbirosei LMG 23360

Align PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 (characterized)
to candidate WP_038018222.1 HA49_RS13180 PTS sugar transporter subunit IIC

Query= SwissProt::P23531
         (568 letters)



>NCBI__GCF_000757425.2:WP_038018222.1
          Length = 428

 Score =  245 bits (626), Expect = 2e-69
 Identities = 136/421 (32%), Positives = 230/421 (54%), Gaps = 21/421 (4%)

Query: 13  PFFEKISRNIYLRAIRDGFIAGMPVILFSSIFILIAYVP----------NAWGFHWSKDI 62
           P   KIS   ++ AIRDGFIA MP ++  S  ++ AY P            W  + + + 
Sbjct: 16  PVAAKISSQRHIMAIRDGFIAVMPFMIIGSFILIFAYPPFSEDNQFFIARGW-LYIAAEY 74

Query: 63  ETFLMTPYSYSMGILAFFVGGTTAKALTDSKNRDLPATNQINFLSTMLASMVGFLLMAAE 122
           +  L+TPY+ +MGI++ ++    +  L            ++  L+T L ++V FLL+   
Sbjct: 75  KQQLLTPYNMTMGIMSVYICPAISYCLARHY--------RLEGLNTALLALVAFLLICC- 125

Query: 123 PAKEGGFLTAFMGTKGLLTAFIAAFVTVNVYKVCVKNNVTIRMPEDVPPNISQVFKDLIP 182
           P   G   ++++G  G+ TA I A +   + +V  + N+ IR+PE VP NI + F  LIP
Sbjct: 126 PLNNGTMESSYLGGSGIFTAIIVAVLVCELSRVLHQKNIGIRLPEQVPDNIRKSFNQLIP 185

Query: 183 FTVSVVLLYGLELLVKGTLGVTVAESIGTLIAPLFSAADGYLGITLIFGAYAFFWFVGIH 242
            ++ +++L+ + L V+   G+ + ++I  L +PL SA+D    + +        WF GIH
Sbjct: 186 LSLVLLILFPVSLAVQSLSGMLIPQAIMALFSPLLSASDSLPAVIIAVIICHVLWFAGIH 245

Query: 243 GPSIVEPAIAAITYANIDVNLHLIQAGQHADKVITSGTQMFIATMGGTGATLIVPFLFMW 302
           G +IV   + A    N+ +N   + +G  A+ +       F  T+GG+GATL +  L++ 
Sbjct: 246 GATIVSGFLQAFWLTNLGINQSKLASGLPAEHIFVEPFWAFFITLGGSGATLGLVLLYL- 304

Query: 303 ICKSDRNRAIGRASVVPTFFGVNEPILFGAPIVLNPIFFVPFIFAPIVNVWIFKFFVDTL 362
             KS   R+IG+ S+VP+ F +NEP++FG+PIV+N +FF+PFI  P+VN  +  F +   
Sbjct: 305 RSKSAHLRSIGKISLVPSLFNINEPVIFGSPIVMNTLFFIPFILTPVVNAVLAWFAIKYG 364

Query: 363 NMNSFSANLPWVTPGPLGIVLGTNFQVLSFILAGLLVVVDTIIYYPFVKVYDEQILEEER 422
            +    +  PW +PGP+G    T + + + +L  +LV    +IYYPF K+Y+  +L EE+
Sbjct: 365 LVAHIVSLAPWTSPGPIGAAWATGWDINAALLVLVLVCSSALIYYPFCKLYERSLLAEEQ 424

Query: 423 S 423
           +
Sbjct: 425 N 425


Lambda     K      H
   0.324    0.140    0.414 

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: 572
Number of extensions: 26
Number of successful extensions: 5
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: 568
Length of database: 428
Length adjustment: 34
Effective length of query: 534
Effective length of database: 394
Effective search space:   210396
Effective search space used:   210396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 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