GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Klebsiella michiganensis M5al

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 BWI76_RS07535 BWI76_RS07535 dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Koxy:BWI76_RS07535
          Length = 347

 Score =  266 bits (679), Expect = 7e-76
 Identities = 140/323 (43%), Positives = 213/323 (65%), Gaps = 11/323 (3%)

Query: 4   DQGGIKMKPLLQTVDLKKYFPQG----KRILKAVDGISIEIKEGETLGLVGESGCGKSTL 59
           D GG   +PLL+  +L K+FP G    + +++AVD +S  + +GETLG+VGESGCGKST 
Sbjct: 8   DLGG-PAQPLLKVNNLLKHFPAGGGKAREVVQAVDDVSFAVIKGETLGVVGESGCGKSTT 66

Query: 60  GRTILKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIED 119
            R +++LL+ D G++ F+G ++ + +   MK YR+++Q++FQD   SLNP+MT+   I  
Sbjct: 67  ARLLMQLLKQDSGELIFDGLEVGS-SRLPMKAYRRQVQMVFQDSYASLNPRMTMEESIAF 125

Query: 120 PLIIHKIGTKKERRKRVEELLDMVGIGRE-FINSFPHEFSGGQQQRIGIARALALNPKFI 178
              +H +  K E  +    LL  VG+  E F + +PH  SGGQ+QR+ IARALA+ P+ +
Sbjct: 126 GQRVHGVSAK-EASEYARYLLAHVGLEPERFAHRYPHALSGGQRQRVNIARALAMKPRLV 184

Query: 179 VCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEY 238
           + DE VSALD S++AQ++ LL+E+++ + ++Y+FI+H+L VV  +S ++ VMYLG++VE 
Sbjct: 185 ILDEAVSALDKSVEAQVLQLLQELKRTLALTYVFISHDLHVVRWLSDRILVMYLGEVVEI 244

Query: 239 GDVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYS-LKGELPSPIDLPKGCRFQTRCTE 297
           G  +++F    HPYTRALL S+P +  D   +   S L G+ PSPI  P GCRF TRC  
Sbjct: 245 GPAEQLFTASAHPYTRALLSSMPSM--DPHNRTLTSALNGDPPSPISPPSGCRFHTRCPH 302

Query: 298 KKAICFEKEPELTEVEKNHFVSC 320
            +A+C E +P L  V + H  +C
Sbjct: 303 ARAVCAEVKPTLQSVGEGHQSAC 325


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: 318
Number of extensions: 18
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: 328
Length of database: 347
Length adjustment: 28
Effective length of query: 300
Effective length of database: 319
Effective search space:    95700
Effective search space used:    95700
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