GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pantoea rwandensis LMG 26275

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_084934899.1 HA51_RS12950 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_002095475.1:WP_084934899.1
          Length = 367

 Score =  267 bits (683), Expect = 3e-76
 Identities = 151/345 (43%), Positives = 206/345 (59%), Gaps = 18/345 (5%)

Query: 1   MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60
           M  ++L ++ K +GE + +  +  D  +G FV  +GPSGCGKSTLLR IAGLE    G+I
Sbjct: 1   MSHLSLHHITKAWGEKIALNDISFDAAEGSFVALLGPSGCGKSTLLRTIAGLETADSGEI 60

Query: 61  MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120
                D T +PP++R L+MVFQSYAL+PH+ V++N+ F L+    + Q    R+ + +K+
Sbjct: 61  HFKHSDITHLPPSQRKLSMVFQSYALFPHLNVRENLLFGLKARGEDKQTFTTRLDDVSKL 120

Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180
           + L   LDR P QLSGGQ+QRVA+GRA++      L DEPLSNLDA LR +MR EI  L 
Sbjct: 121 MELDKLLDRLPSQLSGGQQQRVALGRAVIANNNLCLMDEPLSNLDAKLRQSMRREIRALQ 180

Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240
           + L  TM+YVTHDQ EAM+MAD I++LN G IEQ G+P  LY NPA +F A FIG+P MN
Sbjct: 181 KKLALTMLYVTHDQTEAMSMADSIILLNDGHIEQHGTPNDLYNNPATIFAAQFIGAPPMN 240

Query: 241 L--------------IEGP--EAAKHGATTIGIRPEHIDL-SREAGAWEGEVGVSEHLGS 283
           +              ++ P  E     A ++G+R E I L S +  A    V   E++GS
Sbjct: 241 ILPLHAKGEQHYLSHLQTPVVERCDEVALSLGLRAEDIQLISADNAALTARVISYEYMGS 300

Query: 284 DTFLHVHVAGMPTL-TVRTGGEFGVHHGDRVWLTPQADKIHRFGA 327
           DT L   +AG+  L TV+  G      G  V L   A + + F +
Sbjct: 301 DTLLACQLAGLSELVTVKVPGMQRYDEGSLVGLQWSAARQYLFSS 345


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: 272
Number of extensions: 13
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: 332
Length of database: 367
Length adjustment: 29
Effective length of query: 303
Effective length of database: 338
Effective search space:   102414
Effective search space used:   102414
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