GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Flavobacterium ummariense DS-12

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_091525325.1 BM253_RS13430 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_900115115.1:WP_091525325.1
          Length = 585

 Score =  102 bits (254), Expect = 2e-26
 Identities = 75/225 (33%), Positives = 119/225 (52%), Gaps = 13/225 (5%)

Query: 2   GKITLRNVQKRFGEAVV--IPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQ 59
           GKI  +NV   + +  +  + ++   I +GE V F+G +G GKST+L+LI+ L DVS G 
Sbjct: 340 GKIEFKNVHFIYEDTKIHALNNISFTINEGETVAFLGKTGSGKSTILQLISRLYDVSSGS 399

Query: 60  IMIDGRDATEM--PPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNA 117
           I ID  D  ++     +  +A+V Q   L+   T+K NI F    A  E  E   ++++ 
Sbjct: 400 ISIDNIDIKDLNVENLRDQIAVVPQDAFLFSD-TIKNNIQFGKENASQEEIEHFAKIADV 458

Query: 118 AKIL-----NLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNM 172
            K +          L  R   LSGGQ+QRV+I RA++++    L D+ LS +D      +
Sbjct: 459 HKNIMRFEKGYDTILGERGITLSGGQKQRVSIARALIKDAPVLLLDDCLSAVDTETEERI 518

Query: 173 RLEITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGS 217
              + ++  S + T I VTH +V +   ADKI++LN G I + G+
Sbjct: 519 LNNLKDI--SAKKTTIIVTH-RVSSAKNADKIIILNDGEIIEQGT 560


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: 345
Number of extensions: 10
Number of successful extensions: 3
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: 585
Length adjustment: 32
Effective length of query: 300
Effective length of database: 553
Effective search space:   165900
Effective search space used:   165900
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: 51 (24.3 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