GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Rhizorhabdus wittichii RW1

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  137 bits (345), Expect = 3e-37
 Identities = 80/225 (35%), Positives = 130/225 (57%), Gaps = 12/225 (5%)

Query: 21  AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI-------DGKVVNDV 73
           A++N +L V   E +V+ GPSG GK+T +R I GLE   +G I I       D +V+  +
Sbjct: 16  ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRVLQRI 75

Query: 74  EPKDRDIAMVFQNYALYPHMTVYENMAFG-LKLRKYPKDEIDRRVREAAKILGIENLLDR 132
             +   + MVFQ++ L+PH+T+ EN A   +K+R   +D  +   RE  + + I +  D+
Sbjct: 76  RAR---VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADK 132

Query: 133 KPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIY 192
            P QLSGGQ+QR A+ RA+   P++ LFDEP S LDA++  ++   +K L      T++ 
Sbjct: 133 YPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GITMLC 191

Query: 193 VTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFI 237
           VTH+   A  +AD+I+ M  G+I + G+P + + +P +     F+
Sbjct: 192 VTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236


Lambda     K      H
   0.319    0.138    0.387 

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: 199
Number of extensions: 7
Number of successful extensions: 4
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: 369
Length of database: 241
Length adjustment: 26
Effective length of query: 343
Effective length of database: 215
Effective search space:    73745
Effective search space used:    73745
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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