GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Chryseobacterium viscerum 687B-08

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_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_002899945.2:WP_103234822.1
          Length = 416

 Score =  171 bits (433), Expect = 3e-47
 Identities = 97/281 (34%), Positives = 163/281 (58%), Gaps = 21/281 (7%)

Query: 20  VAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVND------V 73
           + +  A+  + + EF V++G SG GK+T LR +  L E T GK+YI+   +        +
Sbjct: 49  IGINKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYINDDDITSKNNKELL 108

Query: 74  EPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRK 133
           E +  +++MVFQ + L PH T+ +N  FGL++R   K   + + ++A  I+G+    ++ 
Sbjct: 109 EVRRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNGFENQY 168

Query: 134 PRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYV 193
           P QLSGG +QRV + RA+  +P+V L DE  S LD  ++ +M+ ++ +L + LQ TI+++
Sbjct: 169 PSQLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTLQKTIVFI 228

Query: 194 THDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGF---------IGSPPMNF 244
           THD  EA+ + D+IV+MKDG I+QIGT  +I  +PA+ +V  F         I +  + F
Sbjct: 229 THDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFVEKVDRKTIITARSLMF 288

Query: 245 VNARVVR-----GEGGL-WIQASGFKVKVPKEFEDKLANYI 279
             A VVR      EG L  ++A+G +     +F++K   ++
Sbjct: 289 DKATVVRFRKDGPEGALRKMRATGLENLPVVDFQNKFLGFV 329


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: 349
Number of extensions: 14
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: 369
Length of database: 416
Length adjustment: 31
Effective length of query: 338
Effective length of database: 385
Effective search space:   130130
Effective search space used:   130130
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: 50 (23.9 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