GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Brucella inopinata BO1

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_000182725.1:WP_008510542.1
          Length = 333

 Score =  407 bits (1046), Expect = e-118
 Identities = 203/332 (61%), Positives = 250/332 (75%)

Query: 1   MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60
           MG + L++V KR+G   V+  ++L++ DGEF++FVGPSGCGKSTLLR IAGLEDVS GQ+
Sbjct: 1   MGSLQLKSVHKRYGAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQV 60

Query: 61  MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120
           +I+G D T  PP++RG+AMVFQSYALYPH+TVK N+   L+ A     EIE RV+ A+ +
Sbjct: 61  LINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAM 120

Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180
           L L  YL RRP +LSGGQRQRVAIGRA+VR P  FLFDEPLSNLDAALRV  RLEI +LH
Sbjct: 121 LALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLH 180

Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240
           + L+ TMIYVTHDQVEAMT+AD+IVVLNAGRIEQ+GSP+ LY  P NLFVAGFIGSP+MN
Sbjct: 181 RELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQMN 240

Query: 241 LIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPTLTVR 300
            IE       GA TIGIRPEH+ +SRE+G W+G+V  +EHLG+DT L+V       +T R
Sbjct: 241 FIEAARIGATGARTIGIRPEHLSVSRESGTWKGKVIHAEHLGADTILYVETETAGLVTAR 300

Query: 301 TGGEFGVHHGDRVWLTPQADKIHRFGADGKAL 332
             GE   +  D ++LTP+  K H F   GKA+
Sbjct: 301 LFGEQHYNEDDVIFLTPEEGKTHYFDEAGKAI 332


Lambda     K      H
   0.320    0.137    0.400 

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: 381
Number of extensions: 10
Number of successful extensions: 1
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: 332
Length of database: 333
Length adjustment: 28
Effective length of query: 304
Effective length of database: 305
Effective search space:    92720
Effective search space used:    92720
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 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